Notice how I was having the problems in Windows 7 features itself, and also other programs unrelated to windows, that program was Source SDK.
I have no clue how or why this is happening, and I really need to solve it.
Those symptoms seem to be related to a trojan that was released a while back that would mimic keyboard/mouse strokes uncontrollably. I don't remember the exact name, sorry I've slept since then. When you ran MalwareBytes, did it return any sort of trojans or whatnot? You may want to do a full deep scan if you didn't previously and also employ another scanner such as Spybot Search & Destroy. You could possibly even do a sfc /scannow if you have the Windows CD and see if it will repair the files that might be damaged.
Download AVG Rescue CD http://www.avg.com/us-en/avg-rescue-cd and boot your system to that and run a scan on your hard drive without the OS running. After that completes, as mentioned above, run sfc /scannow to verify none of the OS files are corrupt/missing. When that completes reboot and run Malwarebytes.
Good + Bad News
None of the above methods helped me out.
Although I found out that these problems only occured on the User Account that I was on, so I made a new admin account and deleted that one to avoid those problems.
So this problem just remains a mystery now.