I would create a blank ThinApp with just CMD link. Then install the app natively on the VM and and run the CMD/ThinApp to then launch the apps executable.
If this works, then I would start using some tools the monitor the processes and services.
What kind of application is it?
Does it require a server communication?
Does it need system drivers?
Is this an in-house application?
VMware EUC by Broadcom
https://techzone.vmware.com/