i have found that occasionally my swap directory gets reset back to /tmp (i am using 3 SSDs and i had configured PI to write files to those 3 SSDs, none of which are /tmp)... i don't know if this is an actual bug, or perhaps when upgrading PI the settings got reset, or what, but it's worth periodically making sure your swap files are not being written to /tmp when you first fire up PI. i don't think the directory gets reset if it's been set while PI is running - it seems to have gotten reset between launches.
rob