Hi, Todd
If your encoders have Index Puls output there are a couple of cards you can use to be right on every time.
If not then try slowing the "Speed %" down in Config, Homing/Limits, default is 20 % of max speed.
Increasing your "Kernel Speed", Config, Ports and Pins, Port Setup would give Mach more scan time to look at your OPTO Inputs.
Changing kernel speed requires restart of Mach and re-tune of motor tuning, I think.
Just some Thoughts, Chip