UPDATE: As promised, here I am to report on my findings.

I went into the BIOS and turned off everything I could think of. I then tried the computer out for 48h and the problem disappeared.

I then turned on the on-board audio, and waited another 48h. Flawless.

Finally, I turned on the USB Controller option and, again, no sign of any problems for the next 48h.

Today, I turned on the "USB 2.0 Support" option... and about 2 to 3 hours after, the CPU jumped to 100% and System Interrupts is the culprit, as expected.

I still haven't turned everything on (like "USB Legacy Support" for instance) but it seems I've found the problem... my question now is, how do I fix it?

Well, turning it off works, of course, but how can I have 2.0 USB support without going into the BIOS? Is there a way to fix this other than to buy a new mobo? And while I'm at it, what could have caused this?