Mach 3 probe issues

Im playing around with adding a probe and using some of the probing functions in mach 3. I have a 1/2 dowel set as tool 99 and it works fine for touching off the surface when used with the avid touch plate. All of the other probing functions will not work though when there is a height offset applied to the tool. It starts moving but then it freezes. I can zero out the tool offset and probing works, but then I cant use it to touch off the surface of anything, all the tools in my atc with be incorrect. Any thoughts?