Song Mode: Convert>Sequence Bug

When I convert>sequence in Song Mode, the sequence I get has missing sounds, as if some pads were muted, but I don't have anything muted. This only happens in certain parts of the new sequence. Has anyone else experienced this?

All the tracks that are being used have the same assignments. I have some unused tracks that are different from sequence to sequence, though.

They're there as leftovers from getting the song together, experimenting with sounds. I will take all unused programs, samples, etc. out and see what happens. I'll reply with how it goes. Thanks!