Is the "host" switch in the right place?
Does the midi file use the Yamaha standard of bank switching (i.e. both controllers 0 and 32)?
Is there any non-Yamaha system exclusive data being sent?
Does the Yam playback the same midi file from a floppy?
Does the Yam work with other midi files?
If you create a song from scratch in Logic does this playback on the Yam?

Is that enought to be going on with?!?!?!?!