and do a test with everything except USB unplugged. Incorrectly wired things like limit switches for example, can prevent the board from running properly (if your limits are not wired as shown in docs.openbuilds.com they can short 5v to gnd for example - quick test, unplug all the connectors, just leave USB then you tests PC+BlackBox without external factors)
Most likely switches if you have the regular switch kits: OpenBuilds BlackBox 4X Documentation. Avoid the temptation to use 3 wires, use 2 as shown in the documentation(2 is fine because BlackBox has awesome onboard noise filtering circuitry) Or upgrade to the Xtension limits: Xtension Limit Switch Kit, way easier to wire up: OpenBuilds BlackBox 4X Documentation