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When trying to launch a published application in XenApp 6.x, the following screen appears for a minute, then disappears without launching the application.

This is because the default XenApp 6.x application launch timeout is set to 60 seconds.
The resolution is to set the timeout to a greater value using the following registry key:
Key: HKLM\SYSTEM\CurrentControlSet\Control\Citrix\wfshell\TWI
Type: REG_DWORD
Value Name: LogoffCheckerStartupDelayInSeconds
Value Data: 600
The example above sets the application timeout to 10 minutes. (the value data is in seconds)