App volumes inserts a whole lot into the registry even if the app volume is completely blank
As you can see those SnapVolumes registry hives are essentially entire copies of the registry and causes weirdness in a lot of situations. Open EventVwr if you have any appstack attached and watch the slowness for an example.
As for a fix you might be able to use this key:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\svdriver\Parameters\HookInjectionWhiteList and add the executable for the software you are using into that. This may make it so the application itself doesn't see what AppVolumes does. You will probably have to have the application in your base image though if you do this.
Are you using the same image for both your master image, and the image you are capturing AppStacks on? If not, try re-capturing the AppStack on the master image.