While I would certainly look for malware on your system, Im not sure thats where I would focus.
Did you make any changes to your system? Even something small? Installed any new applications? Move a cable?
Can you run a memory benchmark - this should validate the system is ok before you move onto graphics testing...Does CPUz match what you think your system is doing?
Pick any sort of benchmark tool and run GPUz in the background - what are the GPU clocks doing? Does the benchmark run? Are they correct? Are they increasing with 3d and falling back when done? Are they at the right speed?
Remove one of the 4890's and see if it works right. Swap and look again.
4890's do not run at 45C - thats idle speed (unless you are using water). Whats the temp while playing?
The temp while playing is around 70° C. I doubt that its a overheating problem, i have an antec 1200, so full of coolers. Next to that i have the HD4890 formula editions where the cooling is in the center of the card and not on the far right.