I guess the App-V path are excluded from AppStack template by default. Please try the below steps to include them.
1. Manually attach the AppStack template.vmdk as a new hardware to a clean machine with no App Volume agent installed. Make sure to select "Persistent" changes when attaching.
2. The template shows as a new drive in My computer. Open snapvol.cfg file using notepad
3. Search for App-V and look for the line excludepath= that excludes the App-V folder path
4. Comment out the App-V excludepath path by adding # at the beginning of the line
5. Save snapvol.cfg
6. Remove AppStack template
Use the above template to recapture the application and post the results.