Secondary HDD issues

Hi, I don't know if this is the right area to post this question, so i apologize if it is not in advance. I recently bought and OCZ Vertex plus 60bg SSD just to use for the operating system and various other programs, i already had a Samsung Spinpoint F3 1TB which had everything on it. I installed win7 on the SSD and set it to first boot priority and it works fine. The issue I'm having is, a fair amount of my games and programs won't work when launched from the second HDD anymore, Skyrim crashes instantly, but others such as Crysis 2 still work. The old Windows installation is still on the F3, Would this be affecting it? what would cause the programs to crash? thanks!