@twyce This is with only a single MIDI cable directly connecting both machines, right? No other MIDI or USB MIDI connections are hooked up in these examples?

This might sound a bit silly, but have you tried using a different MIDI cable?

What I think is happening is that some of the MIDI clock messages that the RYTM sends somehow get “dropped” before they are interpreted by the MD.

Do you have a powered MIDI Thru or Merge box you can put in between the RYTM and the MD?