No, they're exactly the same versions and files. Apple computers are using Intel processors for a couple of years now. This means OS X can handle Windows DLL's easier. You're seeing more and more games coming to OS X. Steam, the excellent porting of Feral Interactive, etc.
This doesn't mean that the software reacts the same way on both operating systems though. For example, I bought Feral's Arkham City for OS X. It was really laggy and unplayable. Got a refund, and bought the Windows version, which runs smoothly on full HD. Even if it's the exact same computer.
There seem to be more calculations when running (original Windows native) games under OS X. It could be that this is where more problems are created under OS X.
But this can be disputed as well, since there are a lot of Windows problems reported as well and my version runs perfectly under OS X (after 6 very, very frustrating months...)