I installed a miniserver using a 2.5 WD Sata HDD. I noticed that the disk will park shutdown and restart every 10 seconds or so. This was far worse than what happened here: http://www.sgvulcan.com/load-cycle-count-of-western-digital-green-drives-and-how-to-fix-it-from-linux/
I’m pretty sure this bug is the cause but the only mention was that the apm value of 128 didn’t work on me. Since this is an always on desktop system I just set it to 254.
For good measure I used the idle3 tools as mentioned in the first link to change that too.