OK - I believe this issue is Control software update related. For the second time I've walked into my shop first thing in the carve day and began with a Home All. The Y slave motor did not move resulting in a twisted gantry even with an abort within 5-6 seconds. The first time I had no clue why and just went thru every setting but did not log what I had to change - chalked it up to newbie knowledge voids. This morning's event was immediately after updating Control to .164. What I noticed in troubleshooting is my Firmware had defaulted back to being listed as Grbl 1.1f when I had configued it to 1.1g previously. I set it to 1.1g (it reflashed of course). Now Y slave works well. When I have a chance later this week I will roll back to an earlier version, set it correctly and then update to see if the issue pops up. I also probably need to replace my X axis extrusion or examine my v wheels very closely - X makes a horrible sound while moving even after readjusting all v-wheels.
Grbl does not support software control a second motor, its strictly 3 Axes. The slave motor is slaved in Hardware so CONTROL cannot have an impact, neither likely is firmware settings. If your primary Y is moving then its getting all the commands do so, so the second motor not going too, is hardware: (STEP/DIR./ENABLE is just wired parallel to the slave driver usually via jumpers or switches) - Check second motors wiring - Check current adjustment, to weak or too hot both leads to missed steps (Driver will shutdown on overtemp)