i had simmilar issue related to swap. Swap partition was mounted but not used by system.
swapon -f fixed the page size. After reboot everything was just fine and PLEX was able to index all my media.
Btw. even without swap, memory was never fully utilized on my devicebut the device was just laggy.
However, you are mentioning that you have plenty of free ram, so it also might be something else
