Hi Paul, I run MD through MnM all the time. I’ll check this out on my gear asap, but some basic troubleshooting first:
Check the filter on your MnM Thru machine. Is it completely open? Any Q or offsets that are nonzero?
How about your INP level on the synthesis page? The VOL on the Amp page? Try them both at default settings.
Re the cables, is your gear mark 1 or 2? Don’t know if unbalanced cables would matter here, but the outputs on mark 1 models are not balanced, mark 2 are.
… If none of this helps, try creating a new pattern and kit from scratch on the MnM and set it up per the manual again, see if you still have the same trouble.