Where is the fountain of knowledge for learning about CNC setups / understanding them

[Doddy]

However, to me it sounds more like a glitch in the electronics side. My next step would be to try a different power supply, or hook up an oscilloscope to see what was going on.

I tend to agree - but am not convinced yet that this isn't an interaction between the electrical side and the mechanical side. I fear a scope is literally beyond the scope of the investigation so far, and a PSU should show problems simultaneously on jogs on two concurrent axis (and likely exacerbated by such).

OP: Are you familiar with microcontrollers?, I'm thinking in particular I could knock you up an arduino sketch to generate a pulse train to step an axis over a predetermined distance, reverse, etc. Even check out the effects of pulse-width and so on. This would give a health-check on the machine from controller through steppers (including PSU). But for this you'd have to be happy with how to program an arduino and how to connect it to the parallel port interface on the controller (3 wires - ground, step, dir).