I seem to be having a problem with input in certain programs (Games, DOS Programs) that I never had before.
Recently at my house I decided to format all my computers as I finished Highschool and I wanted my PC and Laptop reinstalled so I could start Fresh for College.
Unfortunately, I've been having massive problems with Input lag since the reinstall

The DOS problem is Easy to fix, I have DOS Box which is great. But other things I get lag from, I don't get Lag from Office 2007 or typing on Firefox, just in some programs. I've turn up repeat rates, mouse speeds, everything I can think of. I've Scanned with Esets NOD32 and MalwareBytes with the latest Updates, I've tried different Mice, Keyboards, and even another computer (My laptop) and I can't find the source as to what is causing it. I don't think it's a hardware issue as I find it hard to believe that both my PC and my Laptop have the exact same issues.
On my Brothers Computer (SP2) they all work fine.
I need help badly with this, this lag is driving me up walls. I appreciate any help anyone can give me.