My mistake, I suppose I used a save that had gotten wiped, and then tested with bsnes before using a freeze to restore its data. It's Richard Bannister's port that doesn't maintain compatibility, which sucks because it's fantastic otherwise.
By the way, since you passed by, were you aware that bsnes/Qt does not recognize USB controllers? I was wondering if that was a limitation of Qt, or maybe perhaps you haven't implemented it for the OS X port yet.
I'm also curious about the separate cores. Choosing accuracy core doesn't actually slow down speed much at all. In fact, I maintain a steady 60 fps most of the time. Is the OS X port locked into compatibility or performance no matter what you choose in the preferences? When I use Bannister's port, choosing accuracy gives me about 3-5 fps.
In any case, excellent work.