I think problem is:

• an %Appdata% sub with attributes.ini containing DirectoryIsolationMode=WriteCopy
  

WriteCopy isolation mode means that:

• Modification to virtual elements go to the sandbox
  
• Modification to system elements go to the sandbox
  
• New elements will be created on the sandbox*
  

You need to change it to Merged so these rules will be applied:

• Modification to virtual elements go to the sandbox
  
• Modification to system elements go to the system
  
• New elements will be created on the system*
  

* - your SAP creates new files and those are stored in sandbox which is not accessible by native installed/other virtualized applications. Those are able to be accessed only by virtualized SAP. When you change this behaviour new files will be stored at the system and all applications will be able to access them.

Change it, rebuild package, delete sand-box, and try it.

Let us know,