Before you run down to your servers and upgrade or install the latest release of Citrix XenApp version 6, please check out these know issues with running XenApp 6 on Windows Server 2008 R2, if some of these would be a potential showstopper for you, then I urge you to check out the Citrix Support Forum or the Citrix eDocs

• On Windows Server 2008 R2 platforms, logging off MSN Messenger using the X button on the Messenger window fails to close the application. When you do so, the application minimizes to the system taskbar, which is not accessible with Windows Server 2008 R2.

  As a workaround, with administrative privileges, you can configure Messenger to run in Windows XP compatibility mode for all users. To do this, from the Windows Start > All Programs menu, select Windows Live Messenger. From the right-click menu, select Properties. On the Compatibility tab, choose “Change settings for all users.” Then check “Run this program in compatibility mode for” and choose “Windows XP (Service Pack 3).”

• When using XenApp in a Novell Directory Services for Windows environment, XenApp servers experience reduced performance when enumerating published resources and during application launch when resolution to the least-loaded server occurs. As a workaround, modify the following registry key:
  • Key: HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Citrix/IMA\
  • Value Type: DWORD (32-bit)
  • Value Name: DisablePasswordExpiryCheck

  Be sure to set access control lists (ACLs) for the Network Service account to “Read.” When this workaround is implemented, the number of simultaneous user logons is reduced. Therefore, users might experience longer logon times during peak usage periods.

• The Cumulative Server Load counter (available as part of the Citrix MetaFrame Presentation Server performance monitor counters) might not display the same values as the XenApp command query farm /load (also known as qfarm /load) when querying the same server running Citrix XenApp if there are pending connections to this server. The counter and command should display identical information once all sessions are active.
• In some instances, when a user launches a published application, two Status Indicator icons might appear on the Windows Taskbar for the single published application. The second icon disappears after a few seconds. No workaround exists for this issue and it does not interfere with published application functionality.
• If an administrator specifies a specific Windows theme for users through a Personalization group policy template, the Windows theme might not appear to be applied when launching a published application configured for seamless or non-seamless windows. (Any configured themes are correctly applied when launching published desktop.) To ensure themes are applied, administrators can modify the Windows registry. For details, see https://support.citrix.com/article/CTX124407 in the Citrix Knowledge Center.
• On XenApp servers running the German language version of Windows, after configuring Citrix policy settings for a Group Policy Object, the Settings report for the Group Policy Object does not display the Citrix policy setting values when generated. As a workaround, use a language version of Windows other than German to view the policy settings values.
• The Group Policy Results report does not include Citrix policy settings when run on a Group Policy Object (GPO) that meets one of the following conditions:
  • The GPO contains both a Citrix administrative template (.adm) and Citrix policy settings
  • The GPO containing Citrix policy settings inherits the settings of another GPO that contains a Citrix administrative template

  To resolve this issue, use separate GPOs for Citrix policy settings and administrative templates and ensure these GPOs do not inherit settings.

• In user environments where Citrix Receiver is installed and Microsoft Windows 7 Specialized Security Limited Functionality (SSLF) templates are applied, Citrix Receiver might not run automatically at user logon or startup. Additionally, any installed Citrix plug-in and client software might not launch automatically at user logon or startup. The suggested workaround for this scenario for administrators is to remove the CitrixReceiver entry from the registry key HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run and deploy the Citrix Receiver software through the user’s Startup shortcut.
• When installing the Citrix online plug-in on a user device, pass-through authentication is not automatically configured. To ensure pass-through authentication is enabled for users accessing XenApp Services sites:

  1. On the XenApp server, enable the pass-through authentication method for the XenApp Services site.
  2. Ensure that on the user device, Internet Explorer has the URL to Web Interface added to the local Intranet Zone.
  3. On the user device, add the icaclient.adm file using the Group Policy Editor and configure the following settings:
     • Enable Local user name and password and then select Enable pass-through authentication
     • Disable Kerberos authentication
  4. After configuration, run gpupdate /force, log off the user device, and log back on.

  For detailed instructions about configuring these settings, see https://support.citrix.com/article/CTX113004 in the Citrix Knowledge Center.

• When using Remote Desktop IP Virtualization in per session mode on servers with dual network adapters, virtual IPs are not assigned when sessions are created. This is an issue in Windows Server 2008 R2 that might occur if you use virtual IPs with XenApp. To work around this issue, configure Remote Desktop IP Virtualization to assign virtual IPs on a per program basis.
• The “Pass-through with smart card from Access Gateway” feature cannot be used with XenApp 6.0. Because of an issue with XenApp 6.0, smart card users logging on to Access Gateway integrated XenApp Web sites are unable to access resources when the pass-through with smart card from Access Gateway feature is enabled. Users clicking on a link in the XenApp Web site to access a resource delivered by XenApp 6.0 see the error message “An error occurred while making the requested connection.” You can avoid this issue by configuring the site to prompt smart card users for their PIN each time they access a resource.

• Changes to worker groups might not be reflected accurately in the registry when a worker group is renamed or deleted. The registry entry for the worker group in HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Citrix\IMA\WorkerGroups subkey is not automatically updated.

  As a workaround:

  1. Create a new temporary worker group with all servers in the farm, which forces the registry to update for the renamed or deleted worker groups.
  2. Delete the temporary worker group.
• When generating the Settings report of a Group Policy Object (GPO) linked to the domain, the Group Policy Management console stops working. To work around this issue, access the original GPO, under the Group Policy Objects node, to generate the Settings report.
• For changes to Health Monitoring and Recovery to take effect, in Windows Component Services, Services (Local), restart the Citrix Health Monitoring and Recovery Service.
• For instructions about creating server-side content fetching whitelists for HDX MediaStream for Flash, search Citrix eDocs (this Web site) for the topic “Configuring HDX MediaStream for Flash on the User Device.” Instructions found in the HDX administrative templates are outdated.
• Windows Media Player, when installed on a XenApp server, occasionally hides video behind a black Media Player screen on a user device running Windows 7. To correct this, users should change their Media Player view to Skin Mode. Alternatively, they can minimize and maximize the Media Player (more than once might be necessary) to refresh the video.
• Installing the HDX MediaStream for Flash version 1.1.0 package (CitrixHDXMediaStreamForFlash-ServerInstall.msi) using Active Directory Software Installation might fail. To prevent this failure, use a start-up script to deploy the package.
• After performing a Repair on Citrix HDX MediaStream for Flash-Server, the HDX MediaStream for Flash service might fail to restart. To avoid this issue, uninstall Citrix HDX MediaStream for Flash – Server and reinstall it.

• If you install a role component from the Autorun menu by selecting Manually Install Components and then install the XenApp server role from Autorun, you may be prompted during XenApp role configuration for the location of that component’s server, even though you did not select that component during XenApp server role installation. Re-enter the server information you specified during the manual installation. This also applies during a command-line XenApp role configuration; you must specify the server information for all the installed components.
• The Provisioning Services Target Device software resets your network connection during install. As a result, you may see user interface crashes or other failures if you select this component to install from a network location. Citrix recommends that you install the Provisioning Services Target Device software using one of the following methods:
  • Install from a local DVD image or ISO
  • Copy the installation media locally before performing the installation
  • Select Manually Install Components from the Autorun menu
  • Install with a command-line installation
• You must install the Provisioning Services role and the Provisioning Services Target Device component on separate servers. If you select both on the same server, the installation fails.
• If you install the XenApp server role and then uninstall it, Citrix recommends that you re-image the server with a clean operating system before installing the XenApp server role again. Re-installation of the XenApp server role on a machine where it was previously uninstalled may fail in the following conditions:
  • If you previously created a farm on this machine
  • If you had IIS installed on the machine previously and/or chose to install XML Service Integration with IIS
• If you specify an unsupported Microsoft SQL Server database version during XenApp server role configuration, the configuration fails but the error message may not state the cause. For supported database versions, see the system requirements topic and https://support.citrix.com/article/CTX114501.
• To install the EdgeSight for XenApp Agent, either install it at the same time you install the XenApp server role (and then restart the server after you configure XenApp), or, if you have already installed the XenApp server role, install the agent from the installation media using the MSI file in Service Monitoring\Installers\Agent\. Then restart the XenApp server. If you installed the XenApp server role and later installed the EdgeSight for XenApp Agent using the Server Role Manager, you are not prompted for the agent configuration, and the agent does not report to your EdgeSight server. To provide the proper configuration in this case, uninstall the agent and reinstall it from the installation media.
• If the network connection fails or disconnects during a wizard-based XenApp installation, you may see the error message “Citrix eXtensible Meta Installer has stopped working.” This is typically a non-fatal error; restart the XenApp Server Role Manager and finish your installation or configuration. You can also avoid this issue by copying the installation media locally or installing from the DVD.
• After installing the Delivery Services Console, if you use the Autorun menu to install Applications on Virtual Machines and select Install optional components > Upgrade Management Consoles, a separate console is installed, rather than adding a “VM Hosted Apps” node to the Delivery Services Console.
• When installing the XenApp server role, if the required IIS role services are deployed on the server and you choose not to enable IIS integration by deselecting the XML Service IIS Integration component in a wizard-based installation, or by omitting the XA_IISIntegration option in a command-line installation, you must change the XML service port (to a port other than 80) when configuring the XenApp role.
• When you select both the XenApp and Web Interface roles to install, and the IIS role services are not deployed on the server, the Web Interface role automatically deploys the IIS server roles. However, the XML Service IIS Integration component checkbox is not selected by default. Either select this checkbox or specify an XML Service port other then 80 when you configure XenApp.
• Launching the Server Configuration Tool by double-clicking XenAppConfiguration.exe is not supported. Launch the Server Configuration Tool through the Server Role Manager.
• When using the Server Role Manager to install and configure the SmartAuditor server role from a network share that requires authentication, after restarting the server, log on to the network share