Try deleting the contents of your nvram and cfg folders under your main MAME folder. Warning: this will reset everything to defaults - including all key mappings, resolution settings, etc. If you want to just test this, then move them somewhere temporary rather than deleting them.
Some games get updates to their code from version to version (much change is happening in SEGA code at the moment), and old configurations won't work well with new versions.
If that fails, then head over to MAMETesters and see if it's an official bug. Failing that, the MAME forums themselves.
http://www.mametesters.org/