So you can filter in- and outgoing events, route them between different MIDI ports (but the computer is also a valid destination/source) and change the channels in MIDI data. Plenty of stuff that can cause issues.
According to the manual you use an application called 'Clockworks' to set up and configure the MOTU itself.
Could you verify what preset you are using? Is it one of the factory presets (if so, which one), is it perhaps a user preset? If it is a user preset, how is it set up?
The following image is from the manual.
It shows the channel mapping that can be done. In this case it applies to input on MIDI port 1; channel 1 gets changed to channel 1 (so unchanged), channel 2 gets changed to channel 2 (so unchanged), ... and channel 16 gets changed to 16 (so unchanged). You could however set the channel (after the mapping, so the green box in the horizontal row of 16 dots) to the first dot (channel 1) in every case. If I understand it correctly, then data coming in on any channel gets mapped to channel 1 (so to your computer it would appear as if it is only receiving data on channel 1).
I'm sure you could set up filtering too, so that only data on channel X would pass thru the MOTU, while all other data would simply be ignored.
Regarding your older iMac: I don't think that matters, it think it has nothing to do with the issue you're seeing.
