Have you tracked your cpu temps when you are gaming, or have you done a prime95 or intel burn test?
Sysfan will run your cpu fan, but with no signal from the actual cpu fan header, I think you may be causing issues with bios. It may see the temp rise on the cpu, and keep trying to feed speed through the cpu header. When it encounters difficulty, it may be sending a cutoff signal to the gpu or some such.
Run a cpu stress test and monitor your temps. Also run a gpu stress test and monitor those temps also.