Issue with Windows 7 Ultimate 64 bit and scripted animations.

I recently upgraded to a Windows Ultimate 64 bit system and when I transferred my Unity project folders over I noticed that all scripted animations were no longer working. Default animations on objects work fine but even the included 3d character controller script isn't allowing animations. I'm not sure if it's a java issue or an os issue. Has anyone else encountered this problem?

Edit:

After investigating some more I've learned that it's just random animations not working, scripted or not. Everything worked fine on my laptop with windows 7 32 bit but the same project folders on windows 7 ultimate 64 bit on a pc are screwed up. I've tried using an older version of unity to see if it was a compatibility issue, updated java, updated my video card drivers and even tried the on board video so it's not a video hardware issue. Anyone have any suggestions?