My computer has recently started lagging in minecraft, ever since I installed 3 more case fans to the build.

I know I have no other programs running, and no viruses.

Simplified PC specs:
32GB RAM
GTX 550 Ti (x2)
1TB HHD (7200rpm)
AMD Fx-6300 black 6-core 4.2ghz

I play about 500 FPS, but the game feels very laggy.
I tried vsync/rendering modes/Advanced Open GL

..Nothing

Thanks!