Turns out it was a mod conflict, but it wasn't Engine Light.
I suspect it was Stock Bug Fixes, but I can't be for sure.
I uninstalled Engine Light and it didn't fix the bug.
I did uninstall Chute Safety Indicator, Stock Bug Fixes, and Asteroid Day, and all of the bugs I was experiencing including this bug vanished (I was also having decouplers emit smoke). Since I had no craft using Asteroid Day parts in flight, I assume it was either Chute Safety Indicator or Stock Bug Fixes.
Either way, the problem's solved and RPM is working again.
Thanks for your help.