Ran into a problem where I could NOT get app-v to clear the cache properly on a citrix server.
Set: HKLM\Software\Wow6432Node\Microsoft\SoftGrid\4.5\AppFS\State = 0
Delete all the OSD's in: C:\ProgramData\Microsoft\Application Virtualization Client\SoftGrid Client\OSD Cache
Stop the Application Virtualization Client Agent service (this is a dependant service to say Yes when it asks to shut down the parent service). Note that if you have the client console open at the time (or any apps) you will get a connection error, this is harmless, it's just telling you that, well, you stopped the service and it cannot connect.
Open the client console, refresh the publishing server. Problem should be solved.
A pretty common indicator that an application is stuck in the cache is Error #: 00001004
If you see that error, you probably have some OSD's hung up in the cache. If this STILL doesn't resolve it, make sure that in the user profile(s, if you aren't doing mandatory profiles) the OSD caches are cleared as well. That SHOULDN'T be an issue, it's usually the machine cache that fails to be cleaned up properly.