The new update indeed allows for the carts to be read properly, there are still some issues (3rd save slot gets wiped) 1 & 2 are fine, Wannado is on the right track, i can't really speak for genesis owners such as yourself, but for me Phantasy Star 3 / 4 & Shining Force save as they should. The save issue isn't just specific to Phantasy Star 4 but also Shining Force also.
I don't see why Genesis carts would be any differrent. I thought it maybe an issue with the size of the game but Wannado, who is far more knowlegeable about these things would know. He will probably ask you to send him some Genesis save files.
SNES were working from the start i think, at least thats what most people said, it was always just the megadrive that posed a problem. Let me know how it goes for you, as I've only got those 3 games that have SRAM saving, it would be interesting to know if Sonic 3 works, that is if you have it?