Final version of Legend of Link. Now working correctly on MMC5 boards with 32kb SRAM.http://acmlm.kafuka.org/uploader/get.php?id=5155
My issue all along, was that I wasn't wiping the SRAM. I though by default the $6000-$7FFF region was always 00's, because that's how the FCEUX debugger displays that region. I was performing checks of certain registers, seeing if they were not equal, (set by the player) but what was happening, was by default when first running the game on a wiped SRAM chip, the specific regions being checked were filled with FF's, so my game was doing it's SRAM preparations properly, resulting in the real hardware issues.
All fixed, been confirmed on both the Famicom & Nintendo systems.