Have you ever used a 120Hz monitor recently? That would cause your eyes to perceive choppiness.
If not that, then clean your computer for sure. And if it's not that, try reinstalling TF2 or Windows.
Edit: You said you can get 300 FPS. Is this consistent? One of the comments in Chris's FPS configs says that capping FPS can cause choppy video. TF2 is, by default, capped at 300 FPS. Try setting fps_max to 0 in console, just in case this is the problem.