I've run into a similar problem, came here looking for answers. I'm converting a cheap xvico printer to a duet 3 board. (yes, the board costs more than the entire printer, but it'll work!)
I only have the X and Z steppers connected so far, and the X limit switch. It already wont home properly. I found the limit switch is bouncing erratically when the stepper turns on.
I thought I'd try twisting the stepper wires together, as suggested here, but I look at my printer and find it's using a 6 conductor cord to each stepper. 4 wires for the stepper and 2 more for the limit switch, bundled nicely in a black cord.
I'll replace these wires. A few alligator jumpers to the limit switch and it works properly now.