Hi Dale
Just had a look at the documentation on the C11 Revision 8 board that I have on a machine that is in bits at the minute. The missing wire is from the common adjacent to the three red wires and should go to the return on the 10amp driver amplifier card. I suggest that when you finalise the wiring you get some four core screened wire for the amplifier drives but that is being picky again!
Ok I got the drift the wire that exits at the bottom of your posted picture is the USB - still worth checking that it is OK with the load of the breakout board. Some versions of Windows has a settings screen for the power available at the USB sockets and this could be set incorrectly if your PC has this feature or there might not be enough current available in which case the voltage will dip below the desired 5 volts. DO NOT join to the 5 volt high current supply that comes in mid right of your photo. It would also be a good practice to decouple this supply at the breakout board but it looks as if you are using screened wire. The 0 volts of the break out board and the common earth strip should be joined. DO Not join the usb screen () volts from computer) to anything other than the designated breakout board pin adjacent to the +5 volt usb pin.
This might explain some of the peculiar action. Take comfort in the fact that faults often keep together and when you rebuild a part functioning box the rule has to be check and check again. I also recommend a cup of tea between doing and checking and to make a schematic drawing against which the wiring can be checked. Put a clean copy of the corrected wiring in a plastic bag stapled inside the box when it is working. That way it will be there when or should I say if you need it in the distant future.
As far as I am aware the RoutOut bits should be OK so I would not race off and order replacements until you have reached a dead end.
I am retired and try and check this forum every day so get back if you are still having problems or let us know that it is fixed.
Regards
Pat