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Citrix Not Loading Startup Items

We were running XenApp 5.0, windows 2008 SP2 and Appsense EM.
PNAgent.exe was listed as a startup item for each user in the mandatory profile.
Sometimes this would NOT start even though their profile path had not changed.

Delete the file listed below if the path to the end users appsense repository. (registry hives)
Our Appsense EM policy was set to HIVE (save) out this key to – effectively preventing explorer from launching the startup items.

Remove this registry key from the EM path

When Explorer runs, it creates a registry key called ‘StartupHasBeenRun’ under
a key named after the current session ID in[HKEY_CURRENT_USERSoftwareMicrosoftWindowsCurrentVersionExplorerSessionInfo].
When Explorer exits, it removes the key. If the key already exists when Explorer starts, then it knows that it must have previously crashed or been terminated, so it skips running the startup items.