Well I just took a shot in the dark doing this, but hey its something. I had a feeling that Steam was interfering somehow so I downloaded and installed a crack so I can run it without Steam. So far it seems to be working. Although the trainer is now crashing the game at random moments. The console cheats are still working, and load the save with no issues.
Strange how you say Steam is interfering with the game. Cause I certainly am not having any issues at all while Steam is on while I play and am not using a crack or any mods to the game.