Here are my updates.
I managed to repeat the "stuck at boot" issue a few more times.
It only happened when the Edison Breakout Board was connected to my card and disconnected from the computer.
So it appears some signal was sent back and misrepresented.
This only happened when the system was powered down for a long time(over night), draining our capacitors didn't seem to reduce this time.
Without the breakout board connected to the card with the Edison module there were no longer any boot issues.