@maskedsquirrels said in Multitap works for some games but not for others, Secret of Mana, Looney Tunes B-Ball:

Ok back to the original problem. The SOM version I have is Secret of Mana (USA) [En by FuSoYa v1.0] (Variable Width Font Edition).sfc according to the file name.

It still links player 2 and 3 together.

It is likely that this hack change something in the headers of the rom, resulting in snes9x not recognizing the rom and not applying the right settings to enable multitap. You should try with an official usa or pal rom to make sure.