A friend had a similar issue. We had to do two things. Maybe only one mattered but I'll share.
1. Disconnected from all network drives and printers.
2. Unplugged the USB drives.
I played the game for 100 + hours without problem, then this problem appears.
The game freezes then resumes then freezes every 3 seconds after playing for a minute or so.
I tried re-installing the game, lowering the graphics to low, removing all mods.
This is also not a savegame issue, it happens even in a new game.
Also tried running in windowed mode, did not fix the issue.
I also tried using game booster(to see if a background app is causing this).
I do have the latest drivers and patch.
In game music is still playing during these freezes.
One thing I have noticed is my CPU idles (the CPU load goes to 0%) during the freezing.
Any help is appreciated.