This can be closed. FYI found the answer here:

https://retropie.org.uk/forum/topic/21098/fbalpha-became-slow/16
https://github.com/libretro/FBNeo/tree/master/src/burner/libretro#game-xxx-runs-slowly-why-

"Your hardware is probably too slow to run the game with normal settings. Try the following :

Check if there is a speedhack dipswitch in the core options, set it to "yes". Try setting a value for frameskip in core options. Try disabling rewind, runahead, and anything related to the savestates system in retroarch. Try lowering audio settings in the core options. If it is not enough, upgrade or overclock your hardware.

"

The issue here is there's another rewind option in the quick menu, separate from the rewind option under the settings menu. Why exactly? I have it disabled for arcade games, but its enabled in the quick menu, over writing my option for the settings menu.

Goddam. Glad I got to the bottom of it.

This thread can be closed.