Y Axis missing steps on 300K+ line program

I wanted to give you my final update on this issue.
Eventually I called Mesa Electronics and spoke to them about the G540.
They told me Geckodrive's minimum timing on their spec sheet doesn't work and it really should be more around 3000 or higher.

Basically it involves the fact that the optoisolators aren't individually binned and so they all act slightly differently--so that's why one axis may or may not trigger properly at the specified timing.

All considered he mentioned that you can easily turn the timing up to even 10000 and this wouldn't be an issue if one went overboard.

I think years back people were doing "sherline mode" and perhaps I got a unit that needed longer timing for it to work consistently.
Thus far I've got 3-4 hours of use at 3000 timing and no issues at all.
Machine sounds a little smoother and it's getting me through.