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!

it has nothing to do with secondary HDD, those "stupid" games have to be reinstalled, or at-least save data got to be copied to new c drive
I used to keep games after windows reinstall, but now days games made to specially combat that and annoy you
(The games save stuff in My documents, Games folder to store stuff)