Might have something to do with the External Threat option during the campaign creation part. External threat is designed to spawn a strong enemy when you are close to game completion. Boosting research may trigger that event. I'm guessing of course.
we made it so the cheats only affect your race
Delete C:\Users\usernamehere\AppData\Local\Temp and C:\Users\usernamehere\Cheathappens\Work to be sure any older traces of previous trainer are gone, reboot PC so it clears anything left over in the memory and try again running trainer as admin.