You need to reset all the channels to Patch 0 MSB 0 LSB 0 before playing a different song and also turn off whatever note's are currently playing as well, for MIDI files that are expected to loop usually the author will put such reset commands at the end or begining of the song. If that is not the case then the game's driver usually (hopefully) handles that part...
I don't know much about setting that because I have all these programs doing it for me, so I'd suggest googling SysEx information related to your SC-55 to figure out how to reset the unit before playing back a new song on it.
“I am the dragon without a name…”
― Κυνικός Δράκων