i have the same issues with MD and A4
the problem is the MIDI setup of both machines
you have to be very careful to the routing
[ul]
[li]is send/receive active[/li]
[li]which midichannel is base[/li]
[li]which midichannel for cc[/li]
[/ul]
otherwise one machine can easily destroy patches of the othe machine.
that happend to me so often that i made different setups in the global menu for each machine.
at the moment i setup both to be clock master AND slave so i can connect them either way and the one that has the midicord in the out is always the master
and secondly i put the midi base channels on the A4 on 10,11,12,13 and on the MD on 5-8
as soon as you seperate them and dont let them react on omnimidi messages the problem should be gone
at least for me
just never ever touch this globalslot and make a new one for each setup even if it SEEMS to be the same situation 
thats a part iam still working on cause iam lazy hehe