By looking for answers over the Internet, I got some tips on Microsoft Answers and I'm pretty much sure my problem was caused by Intel Desktop Utilities. I disabled it and the problem stopped, the latency has not gotten higher than 1200 microseconds and usually doesn't get more than 200 (the peaks are around 600). The version I was running is 3.1.4.031a. Hopefully Intel will improve it on the next versions. I also had another issue with it, that I already posted: one of the temperature sensors had a default treshold of zero degrees C, and even if I changed it, the next boot it reset to zero. So I had to disable the notification for that particular sensor.
Just to add some more information, the IDU versions up to 3.2.1.042a are still causing high latency and audio and video drop-outs. It seems that there is less occurrence of the drop-outs, but some still remain.