Error while trying to synchronise audio & midi, Motu 828 mkII

Hi, I've tried lots of things before posting this but am running out of ideas - any help appreciated.
Since upgrading from Tiger to Snow Leopard, my MOTU 828mkII has not been working right. The problem happens in Logic 8 and all other apps I've tried which use audio and midi. (eg Garageband, Live, Reason), but I'm posting here because of the specific error message which only appears in Logic.
An inconsistent length of time after opening the app, which may be anywhere from a few seconds to over an hour, midi input is lost and the above message appears in Logic - though midi output remains working. Often there is a brief high frequency noise at the moment this happens, otherwise audio playback is unaffected even though in Logic the screen freezes until I clear the error message. If I'm recording audio, there is a brief interruption in the recording. Then the message reappears several times in quick succession. The only way to restore midi input is to quit and relaunch the app. Also Logic sometimes crashes on quitting, which of course may be an unrelated issue.
Before installing Snow Leopard I cloned my internal (Tiger) drive to an external LaCie firewire drive and if I boot from that on the same computer everything works fine. There is also no problem on my partner's Macbook Pro running Snow Leopard (installed from the same family pack).
MOTU tech support have been pretty useless, though I've tried all the tricks suggested by them like toggling optical inputs and resetting. I've tried changing FW cables, and running with nothing else plugged in at all. I've re-installed the combined OS update and I'm using the latest drivers. I've also trashed all the MOTU preference files, as well as the system audio device settings preference files. Oh and this happens even if I open a new project and have just 1 audio track and no plugins.
The only thing I can think of now is that something got corrupted when I migrated everything back from the cloned drive after installing Snow Leopard, and I need to erase and re-install everything, but if anyone can suggest anything else to try first I'm all ears!
Thanks for reading this - a bit lengthy but I've tried to give all the info I have.
Kit

Sounds like the MOTU needs to be reset.
Did you leave the MOTU unit plugged in via Firewire when you did the OS upgrade?
Not a good idea as the upgraded system Firewire interface has to initialize and often this sends out a bit of random data.
Disconnect the firewire cable from the 828mkII
Press the Setup knob
Turn the Setup knob all the way to the right, (to Factory Default)
Press the Select knob
Press the Value knob
Power off the interface and plug the firewire cable back in
Power the interface back on
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I solved my own problem by resetting the factory presets:
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p.s.
As a side note, I remember that same error.....
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