The probing module has not been changed in recent times. I had a quick eyeball over the Bore script last night and nothing untoward jumps out at me.
So are you using plugin 3.16?In terms of Mach4, I tend to use one of the development versions. I am currently using 3882. My controller is the IP-A, and I cannot say if there are subtle differences in the plugin for the IP-M.
I am tending to think that the plugin is returning the wrong positions, as neither the backoff position nor the centre are coming out sensibly. Presumeably you have set backoff to a small value, e.g. 0.3mm, yet your probe is backing off some 45mm, which makes no sense.
Ultimately, you may need to add messages to the probing script to see just what values are being returned by the probe, but before that, have you tried a simpler probing operation, such as probing the X position of a part at a known position. Does this give a credible result?
You'd do well to start reading up on LUA scripting.
Allan