Shawn,
With 8+3 folder are you referring the recommended practise of creating package's root directory with 8+3 name and that causing some issues?
Maybe your application has hardcoded paths and need to be sequenced so that during monitoring you install it to the default location (so-called VFS sequence). App-V will map/virtualize all files to the Q: drive but application thinks they are on C:\whatever...
when run at the client.
/Kalle