Ok, I tried a fresh install of zsnes 1.51 but still had the same problem.
I've configured my joysticks to match MAME standard, for 1 is 1 player start, 2 is 2 player start.
5 (credit) is select, and 6 select player 2. All be it I don't have a button for such.
I did modify some of the options in background/layer, as buttons 1 and 2 were used by the emulator for that specific task. I changed them to 7 & 8.
However the issue persists.