I apparently fixed it.
I got a file from a friend (A game trainer (cheat)), because he wanted to know if it worked for me. So I started it up, and it didn't work, and I forgot all about it.
But then today I saw the file, and thought that I'd better figure out why it didn't work.
So I reverse engineered it, and it turns out that it's a virus. An executable containing 3 executables, which are unpacked when you launch it (Without your consent or knowledge).
The executable is an nBinder executable (Program to make multiple executables in to one).
One of them is a fake window making you think that you've got a trainer, but in fact it doesn't do ****.
The second executable copies the third file to C:\Windows\svchost.exe
And the third executable apparently slows down input and disables input.
At least, after I cleaned my system from it, I've had no problems spawning 300 zombies in Left 4 Dead 2 and still have instant input.
So problem solved. I'm gonna test for a few hours, and if I don't get any issues, I'll know that I fixed it
Also, the third executable adds a key to the registry, which makes Windows launch it every time the system boots.