Strange system-wide graphical lag started occurring recently

So, recently some strange FPS started occuring on my system accompanied by a constant 5-6% CPU usage of the SYSTEM process. Approximately every 2 seconds everything but the mouse freezes for half a second. This happens regardless of what I am doing (it even occurs if I have only explorer open) and is also recorded by running applications such as games.

As this never happened before, I immediately suspected that my system may be infected. I disabled all autoruns and restarted my computer in safe mode, then ran a Malwarebytes scan. The scan found no infections, but I still strongly suspect that this may be malware.

When I reboot the computer the lag seems to dissapear for some time and the CPU usage of the SYSTEM process usage goes down to 0-1%. After some time, the lag returns and the system process usage increases to a constant 6%.

Do you have any idea what could be causing this and what can I do? If I don't find a way to resolve this i will do a clean install of Windows.

Do you have an anti-virus program running in the background, and have you run a full scan with it (in addition to Malwarebytes which is not the same thing)?

No, I don't have one in the backgound as it decreases performance, which one do you reccomend so I can do a scan with?

So your computer is basically unprotected? I'd recommend you always have one running but avoid those that can hog resources and/or produce false positives. I have personally used Microsoft Security Essentials for a number of years without any issues, but you will get as many recommendations as you get replies! You can have a look at the security forum here for more detailed discussions on the different options available.

I supplement it with manual scans with Malwarebytes (the free version of 1.75 although most will doubtless recommend the newer version which has always seemed to me to be still in beta in all but name), as well as running Malwarebytes Anti-Exploit Free for browser protection.

Scanned the computer in safe mode with Kaspersky and AVG, both found nothing.
After I rebooted the computer this hasn't happened again yet. What should I do to find the cause of the issue if/when it happens again?