Periodic several second freezes with Raspberry Pi 3

[dankcushions]

I'm getting periodic (about once every few minutes, although it's not consistent) hangs of 2-5 seconds, even on games with very lowly/2d graphics like 'work time fun', and even when the game isn't doing anything.

The pi is running the roms from a USB drive, but my RAM isn't full and it doesn't happen during obvious loads, so i don't think it's necessarily a storage speed issue (unless there's other stuff going on!). the CPU is also down in the low %s when the freezes are happening.

I've rebuilt from the current version, disabled developer logging, but none of the other suggested performance options strike me as being likely culprits, so thought I'd ask here before changing everything from default and getting into a mess!

I temporarily enabled developer logging and got the attached log
(there were two freezes i noticed here about 5 seconds apart, and after the second i exited)