Well rather oddly it seems to have fixed itself, I hadn't touched fs2 in a few days and then decided to fire it up and it's working fine now, have been messing around with my pc a lot in the last few days so not really sure what fixed the problem although i hadn't changed any of the launcher settings so it was probably Vista related. Gotta say have had zero problems running anything on Vista up and till this point (Except google earth, and KOTOR and photoshop and anything else you care to mention).
Oh hang on it was probably that xp partition i just added...