This topic has resulted in multiple threads on the MachSupport.com forum for Mach4.
Most of the discussion appeared to be about how to operate probing, but I am not
sure if your issue still exists. If it does, please:
1) send us an example of G-code that will demonstrate it
2) send us a packaged profile from your system
3) if possible send us debug logs captured while running your code when the problem
occurs
4) make notes about actual ending locations versus expected locations
Instructions for running with debug logging enabled are here:
http://faq.pmdx.com/content/2/3/en/how-to-capture-a-debug-log-file-and-send-to-pmdx.html