Not sure if I'm doing this the right way, but it used to work for me and now (R2.47) it doesn't:
When a tool change occurs on my mill, I run the spindle up the z-axis to give me a bit of room, then change the tool and re-zero the z-axis by running the spindle down until the tool touches. Most times, I also jog the x- and y-axis to find a nice zero-level part of the job. Once that's done, I click the start cycle button and Mach3 moves to where it was when it stopped for the tool change, then carries on.
At least, it used to. What happens now is that the x- and y-axis are jogged way off to the right/back of where they should be. It seems as if Mach3 assumes we're starting from zero on all axis again. Indeed, if I click the move to zero button before continuing then everything is OK. Even if I then jog the z-axis upwards after the goto zero it still all ends up right.
So it seems to me that something is broken in this bit that wasn't before - Mach3 obviously knows where the axis are, but the start cycle overrides that and thinks wherever we are is zero. Hope that makes sense