I'm surprised this thread is so dead, now that Neptune is profitable again, which is just wild!

smoothrunnings, Yeah that info is buried somewhere in this thread.

1) You can replace the beaglebone with a newer one, if you're sure it's not the controller board, but I don't know if the newest one is still compatible. Safest bet is getting an older one off of ebay or such. I have one board that has started acting glitchy with the latest firmware, but otherwise I haven't had problems with it.

2) Yes the cables have to go on the correct direction, with the red or blue stripe facing the exhaust side of the cube and facing port 1 (JP7 on the board, aka the LCD screen port) on the controller. A faulty cube, or cube connected to a bad port on the controller, will cause the whole thing to mess up. Try one cube on each port to narrow it down.