I have found the solution now, and wanted others to know.
As i do run 4 steppers with dual on Y axis, i had enabled motor 0,1,2,3 and set stepper 3 as slave on stepper 1. But as i didnt disable stepper 3 afterwards it was still waiting for the Pokeys57cnc to report a stop on last stepper. I didnt know that mach4 and pokeys communicated at that level as i dont have either servos or closed loop stepper, but log shows that it does.
So disabling motor3 as it was moved as slave on motor 1 fixed the problem and now it runs fine beside probing..