I was about to suggest trying this - the problem is with the new change to fix the FX Overclock setting not being applied on boot.That problem without mentioning that on all games (including simple SNES games and all chips FX, SA-1, etc.) reset when returning to the game from the menu if the "FX Overclock" value is set to "Default".
(I mean, SNES games doesn't reset when returning to the game from the menu if the "FX Overclock" value is set to "20 MHz", "40 MHz" or "60 MHz".)
The code was moved into the main loop, so it now gets called any time you return to the emulation (i.e. exiting the menu). There, it now checks if your Overclock setting is 20, 40, or 60, and if it isn't any of those, it will reset the emulation.