I have figured out what the problem is. I have a drive C and D set up on my laptop. My Laptop has a large D drive and a relatively small C drive. I installed the game onto the D drive thinking that this would be a more economical use of space. It was, of course, I mean on one drive I've got 900 + Gigs of empty space, but it caused this latency issue. Now the game works smoothly in windowed/desktop mode as it should. I only hope this is just specific to SP.
Maybe this will help. I had the same (similar) problem.