Ok, next I’d make sure there’s not another copy of the application on mounted volumes (and unmount most volumes you don’t need during the test).
If you find another copy laying around, you don’t have to get rid of it (either move it to another volume which you then unmount or compress the app and delete it (and empty the trash)). Either way, you make sure there’s not another app having the same bundle ID (com.yourcompany,product) on mounted disks.
At that point, I’m not sure a restart or rebuild of some MacOS component could help (I don’t recall having done that in my prior cases).
Once you’re sure there’s no copy of your app available on mounted volumes, you know the OS can’t deal with a wrong version.
When I tested for those issues, it was mostly a matter of making other versions unavailable to the OS and then tweaking with System Preferences (removing or unchecking references to the app in Privacy tab and re-adding or re-checking them). I’m not sure it worked every time, though, but definitively more than not.
And finally, restore the versions you may have moved to another volume or unarchive them.
Also, have you tried on a new OS install? You can simply partition your internal HD and install a new copy of the OS, or install the OS in a virtual machine. Then, first see whether the problem is there too. If it isn’t, you may customise it until you find a pattern for the issue.