This is my first time playing in a good 6 months, when I played previously, I could play on Ultra, and multiple mods, with no trouble. Now all of the sudden, whether or not the settings are on low or ultra, I get constant 60 fps but every 45 seconds or so it drops to ~10 fps for a few seconds and then pops back up. My loading times as well have gone from previously being around 5 seconds, to now being almost a minute.

My GPUs run at about 50-70% usage (with no overheating), which is odd, because I have seen them get to the high 90s in other games, this makes me think my GPUs are not running properly, although Skyrim is still the only game that this issue persists. My RAM and CPU usage go from 40%-60% in game, so those are not being stressed as well.

I have cleaned up my mods and cross referenced them, none are incompatible with each other, and besides, the game still acts poorly with mods on or off, so I do not think it is my mods.

I have validated the game files on Steam as well with no issues.

Specs:
GPU: nVidia 560 TI 1GB SLI
CPU: Quad intel i5 3.2 GHz
RAM: 2x4 GB
Driver: GeForce 314.07 (Up to date), though there is a beta driver out right now.