Non Steam Games not starting correctly

[PimpinPenguin]

I've recently added my most played games into Steam, cause well it's easier.Never bothered before as Steam kept forgetting them. The problem is when i launch though Steam they act like i've never used them before. For example COD4 won't show my profile, yet if i start it normally it's there. KOTOR won't start, says my Graphic card drivers are out of date and it also doesn't find my settings or saves.Yet when i start normally it's fine no errors. Same issues with Mass Effect and Grid. So can anyone give any insight to how steam could be launching them incorrectly. Also i'm using the Steam Beta could that be the issue?