It's looking like this is probably the reason why the original configurator did what they did. At least I'm getting down to the root of the issue.
Going forward, any advice if I want to improve the homing repeatability of this stepper hybrid by using the drive's index output? There are definitely encoders but there's no feedback loop to linuxcnc. Can I access any signals that PCW is referring to without too much pain involved? Is there a way to fake an encoder by feeding back the position output, or is that just asking for trouble?
I'd love to be able to use the existing homing routines as much as possible, as this is what they're designed to do.