Large amount of files keep escaping the layer

Hi everyone, we already have more than 100 virtual apps in our environment. We successfully use this technique since more than one and a half years. However, since the change of the clients (new hardware and sp2 to sp3 from WinXP) we do have some problems with our virtual apps. One of those is that a large amount of files keep escaping the layer. Even on layers with no exclude. The problem is that changing layers (i.e. a newer app version) do not take effekt because almost all of the older files are still in the base. So our Helpdesk needs to deactivate the new layer, clean the file system, reset and activate the new layer and then things are fine. But what's the reason behind this behaviour? We're still on SVS 2.1.3071 because we've had issues with SWV 6.x during internal test phase on German XP.

Could it be a problem because SVS gets installed and then the machine is imaged? So everyone gets the 'same svs installation'?

Thanks for any hints in advance.
Roland