No the caps lock key is not on, and when I hold down left shift I walk instead of run. Basically it's reversed, how do I revert back. Yes I have tried resetting the keys to default. This is how I have always played and it's really annoying now simce I am a monk and I use sneak all the time.

Hit Caps lock, if you keep it on you will reverse it yet again.

so I have to keep the caps lock on at all times to walk normal? Isnt there a way to just fix it to the way it should be (like it was 15 minutes ago)

Or hit Caps lock then press tab, then while in menu, press caps lock again, then exit. This should effectively reverse it.

I just tried a save I had about a minute prior and it fixed it. so it must have been that one save.

It isn't a save problem. It all depends on caps-lock state when you start the game.