XenApp Published Apps don't start, full desktop is launched instead...

Instead of the specified startup program, the whole desktop is started on a remote desktop connection when you change the "Terminal Services Profile" setting for the user account

Because of a bug on Windows Server 2008 Domain Controllers XenApp Published Apps might not start and a full desktop is launched instead.

This issue can be resolved by the next patch which is available on request from Microsoft.
The KB article title : "Instead of the specified startup program, the whole desktop is started on a remote desktop connection when you change the "Terminal Services Profile" setting for the user account"
The KB link : http://support.microsoft.com/kb/969851

After installing the patch, effected user-account's TS-settings need to be checked and saved/applied once.