Well, I've ruled out the power supply and released the magic smoke from my BoB.
I bought a new 48V power supply and hooked it up. I started the X motor cycling and then ran a G-code.
The stepper dropped exactly the same steps as when using the 24V power supply.
In the process, I forgot my BoB was only rated for 24V through the relay and connected capacitor and, well, a loud POP and the capacitor smoke released.
The BoB still worked with the blown capacitor though. All is not lost on that board. I can always solder on a new capacitor and I have two other boards.
So, different motors, problem exists.
Different BoB, problem exists.
Different Power Supply, problem exists.
Next is drivers but they be spendy.