AdminStudio ( Flexera Software) is available with a " Virtualization Pack"

AdminStudio Virtualization Pack prepares software for reliable application virtualization deployment for both desktop and server applications, with a complete set of virtualization suitability testing, automated conversion, validation, editing and management reporting capabilities. It automates the conversion of MSIs and legacy installers to virtual application formats, ensuring a consistent approach that is up to 9 times faster than using native tools, reducing the cost and duration of a migration project.

Sometimes the conversion from setup.exe to App-V ( and all the steps in between) won't give you a working App-V.

This could happen due to a configuration in the Repackager which you need to disable.
This is the "Replace Files with merge Modules whenever Possible"  setting.

By unchecking this option, you will create reliable package ( don't clean up too much)

You can also make this a default setting by configuring the Options.ini file which is located in the " Repackager"  folder.

Change the following variable: " UseMergeModules=Y"  to "UseMergeModules=N"