I have been having exactly the same problems as you for the past 9 months. I would like to know before I actually reflash the eMMC, whether the problem has resurfaced again since your last post.

For a while I thought it was the following:
* power kernel (42 or 46) with standard voltages (or at the max the lv profile)
* themes
* clockspeeds (I excluded 250, then everything beyond 800)
* swappolube

None of these helped. It used to crop up at random, usually at very high load but even that wasnt very consistent.

I repartitioned the eMMC manually from my PC using BackupMenu's read-write mode, but even that hasnt helped too much.

@mattbutsko:
Power kernel v46 changelog states that u-boot has been disabled and bluetooth support has been added. Thats the only diff between 42 and 46, so I guess it should be identical to using 42.