You don't (that I've read) explain if this a new set-up, or a set-up that did work and has now failed - that's kind of important to understand where you are. The question from A_Camera is relevant in terms of UCCNC controller - but that you're using a BoB suggests its not a AXBB, at least. Can you provide that detail as well?

Your fault description shows a common-mode failure across multiple axis. Yes, it could be a major cockup in the UCCNC configuration - but I'd be surprised. I'd look for a common-mode fault, such as a 5V supply failure (or wiring fault) to the BoB that's allowing it to limp under parasitic power but fails across multiple channels when there's an attempt to draw current - particularly as you describe an inconsistent behaviour.

For me, I'd isolate the controller from the BoB, and then toggle any single axis "step" pin on the DB25 connector between 5V and 0V (just a wire, nothing special) - for preference through a 1k resistor (just added safety) - if the problem remains at this level it's the BoB, or supply to the BoB.

EDIT: A photo of your control box could help.