Zoe,
I take it you are plugging MIDI cables into the MOTU and have the MOTU
deliver the MIDI data in through the firewire port into the
applications in the computer? When I was using a RME Multiface avoided
this scenario for years because it created problems with zipper noise
in my audio (not the same problem as you have, I know). Instead of
scrambling MIDI and audio streaming in the firewire bus I was using a
simple MIDI Link USB midi interface to get my MIDI input into the
software world, thus leaving my audio interface to handle audio full
time on the firewire bus. This solved my problem and the RME sounded
excellent. Just an idea for a troubleshooting.
Per