Well I'd like to help you but I think you're missing something and not showing us. If you can run it from a shortcut then you can run it from other means as well.

Check the ACL permissions and any SHARE permissions and check the SHORTCUT that can run it and duplicate all permissions.

PERMISSIONS/PATH/ENVIRONMENT/SHARES

Are all things to look at. Verify what the shortcut is calling, maybe it calls a different program or a program with a switch or something similar.

If the shortcut can run it then you can duplicate it with other programs, we're just not there to see what the issue is, so you need to check all the variables.