I use the Microlite on my large 4M console and the Microlite handles the traffic without complaint.
You said: " I only connected the MIDI IN connectors from the four MIDI encoder boards (3M and pedalboard) to the MIDI IN on the MOTU Microlite USB interface".
I think this may be your problem. The MIDI OUTs from your Encoders should go to the MIDI INs on the Microlite rather than how you stated the connections were done.