I had the same issue and it helped me to configure $3 =2 as shown in the lasergrbl configuration. See on lasergrbl.com
After several tries and restarts from comteoller board it worked. Maybe try to flash 1.1h and configure $3 new. Its necessary to restart the board after every new configuration.
Thanks for the suggestion. I did try that but was unsuccessful. When you say restart, do you mean to simple power down and unplug it? Also i did end up buying a new GRBL 0.9 J+ and the y axis worked out of the box but it fried the laser driver box. Everything was set the same except it seem to be preloaded with 1.1f. Feel like we are getting close but I am now having trouble locating a replacement for the driver box
It sounds like, the y axis driver has blown
If anybody has connected and / or disconnected the stepper motor whilst live (even at idle) then the backemf will blow the driver board which is irreparable .
The trouble is that by changing stuff about may introduce other issues that plague you even after replacement .
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