New 6.5 Farm on 2008R2.
I have a couple of apps published that work fine. The one that fails is Explorer.exe. If I launch one of the other apps first, then it opens fine in the session. If I launch the app by itself in the session, it says "Starting," and after it finishes the progress bar, it dissappears and nothing else happens. If I launch some other app first and then launch it, it opens just fine.
I suspect it has something to do with the profile not being completely setup before the launch.
The Command Line property is "C:\Windows\explorer.exe" "\\domain\Data\Users\zzz\%USERNAME%" (including quotation marks) and the Working Directory is C:\Windows