I found this was happening after what I would call an "unclean" shutdown mainly related to initial attempts to power my pine64 using a microusb cable and the associated voltage drops causing it to lock up.
Once I wired up my own power cable with a much thicker conductor (speaker wire) and dumped a shutdown widget on the desktop to manage shutdowns and the problem has completely disappeared.
Once I wired up my own power cable with a much thicker conductor (speaker wire) and dumped a shutdown widget on the desktop to manage shutdowns and the problem has completely disappeared.