Just a FWIW, it really, really, really is not a good idea to export power from the PC - it likes to live in its own little world inside its steel box
A decent 5v 1A SM PSU is a couple of ££ at most, you should have the BOB and drivers powered by that and use the PP to run the opto-couplers on the BOB inputs alone, no need for a USB then, USB sucks.
It does sound like you have issues with the DIR signals and if you do then you will have issues with the STEP signals too which could = your problems.
I had a bad BOB, a good one too, it would work fine on a 9v battery (built in 5v regulator) but not a PSU - tore my hair out for weeks on my first plasma with this, in the end they replaced it and away we went - this was from a good UK supplier, not eBay etc, it was not a cheap BOB - just shows that even good stuff can be bad out of the box.
The fact you have ordered a 'scope shows serious intent here, but if it were me, I would likely have binned the bob and started again on a different make - it really is the king-pin in the system.
Can you not go ethernet UC300eth etc?
Ethernet rocks for machine control as its noise immune and reliable.