EDIT: This is about Morrowind, but I can't edit the title.

This is weird. Sometimes it will seem like the game isn't getting the inputs from my mouse (not sure about keyboard). The mouselook will start stuttering, starting and stopping, and it doesn't seem to get clicks either. The problem doesn't occur in any kind of menu or dialog, only when you're I'm looking around the world and time is passing. It doesn't seem to be related to my FPS, which usually stays at 60 while it happens.
It seems to happen only after I've had the game running for a while, and is the worst in interiors, especially in very small confines. I've noticed it in the Balmora's Mages Guild, the South Wall Cornerclub, and the Pelagiad holding cells. It happens all over the place and even outside, those are just the places I remember it being worst.
The mods I'm using are:
Morrowind Code Patch Morrowind Patch Project Madd Leveler All latest versions.
Also, my operating system is Windows 7.
Does anyone have a clue what this could be? I'm completely stumped.