Huge thanks for getting back so quickly.
I can save you the hassle of looking into it though. As I have been playing with it to see whats causing the issue as well. The rom I used had a previous hack applied for more useful Frog items. When swapping the rom to one with ONLY Plus added, it works fine, so the frog hack does not work with plus, and causes this odd lock up. Also, being able to swap roms in the mini while using the same save states is useful, even fixing some of the issues ppl have mentioned for Plus in other locations. I know ppl were upset about not being able to max out the HP (im assuming in NES mode). If you rom hack the game without nes mode, get to lvl 99, then add the nes hack, the save file may provide the max HP amount.
As a side note, as you advised why anyone would use the canoe emulator over SNES9X, thats easy. Interpolation. Ive done everything I can on every game on my mini to use the canoe emu for that reason only. If Not, then the game needs to run in 692 (3x) Height, but 896 width to prevent any odd pixel scaling. This is the best that can be done without interpolation. not perfect at all, but it prevents the shimmer. It does cause every other pixel to be one pixel wider 3x3, then 3x4, 3x3, 3x4 exc.
Anyway, thanks again for all the help ... now I just need to figure out how to get into 1999, as they all just start the fight with Lavos.