Thanks PCW!
Based on recommendations for my controllers, I initially had dirhold=10000 and dirsetup=5000. I doubled those, ran another test run, and no missed steps!

(well, at least not that i could tell)
I do have a small accuracy issue on the X axis, but I'm pretty sure that's hardware related (otherwise i'd expect to see it on all axes)
I'm also going to look into that 'stepgen reset' you mentioned. Not sure I'll need it now, but who knows.
Thanks again!