I never said I was changing direction. It looked like a series of incremental moves with a 100ms dwell. Did not make a difference in what axis.
I did find the problem

And I hate 5 volts.
Had a poor connection on a +volt terminal. It kept getting worse till it finally failed the E-stop signal.
Soldered her up and now better than ever.
Thinking it might have been a computer issue:
It gave me a chance to try out a new computer I am eventually going too.
running @ 75K, It can feed at 200+ inches per minute, Boy am I looking forward to that. Best I get now is ~120.
Still think we need a opto board that has 20+ I/O (spring loaded terminals) with 5 volts on one side and 24 volts on the other would be nice.
Cut down on my use of relays for my stack light too from the ModIO board signal. If anyone knows of one let me know if not I will make my own this winter.
Thanks for scratching your heads, hope this helps others.