AppV - Application (.NET) is slower when sequenced

I've recently sequenced an application (Morello Smart Client). This application requires .NET 2.0 SP1 and will be deployed on a citrix farm.

I sequenced the application on a machine with .NET 2.0 SP1 preinstalled. Also, my Citrix servers have .Net 2.0 SP1. Application appears to work fine.

When multiple users use the app however, some functions become really slow. Users have to wait minutes on actions that would take seconds normally.

After a day of troubleshooting we found the problem is with AppV. When we install the application directly on the citrix server all works fine and fast (also with multiple users).

I looked in the package to see if the app uses many virtualised directories, but it doesn't (except some .ico files). Same behaviour when only using RDP (not citrix).
What could be the cause of this behaviour? Any ideas would be appreciated.

We use the following environments:
MS Application Virtualisation 4.5
Citrix XenApp 4.5 on Windows 2003 Ent.
I also contact the supportdesk of the app but thay are of little help.