In my new 4 axis cnc with Mach3 I’m setting my home limits. Prior to that I ticked the AutoLimitOveride in the Mach3 Settings screen and verified all Limits are working by pressing each one (I have 7) and then hit the Reset to stop the E-Stop message. My Home position facing the cnc is at the back end and to the right.

Since it’s a new machine I didn’t want to do all axis at the same time so I started with the Y&A. In the diagnostic screen I clicked Ref Y and both the Y&A started moving towards the back and when they hit the limits they stopped, I reset the E-Stop and then I was able to jog out.

Then I did the same with the X axis. When she hit the limit the axis stopped but I wasn’t able to jog out. At the same time the following lights were flashing in the Diagnostic screen
EjogY+ M1+Limit, M3+Limit
EjogZ+ M1 M2 M3
EjogA+ M1Home M3Home

I shutdown the cnc and manually backed out. Any ideas whats the problem?