Well, perhaps you are not selecting the game through SSF, rather through MA, which is mounting the cue, etc and then running SSF as the executable, and SSF is using the default settings.ini vs the individual games' ini used when launching the game from SSF, which saves your preferences on a game to game basis, giving you the illusion that it's not picking up on the bios, because a bios file was not chosen for the default settings.ini, and dang this is a long sentence! Test this theory asap and report your findings back here. Cross all your digits...