I would not be surprised if the LED would not flash for incoming system real-time messages.
You could try to run this in a terminal with the midisport connected to the BeagleBone.
ssh root@192.168.7.2 amidi -d -p hw:1,0,0
this would dump the raw midi data coming in to the midisport.
Send me the result of that while you are sending the midi clock (also, try to send some notes to make sure they show up).