Glenn: I had a similar problem (though it might not be exactly the same) last week when I tried to "upgrade" from running Mill .020 to something newer.
The machine would just take off for the north (west) forty so to speak. I looked at everything I could think of...soft limits, configuration stuff.... Finally in a durr moment, I opened up the m6start macro, and it was the same as the one for .020. Then, the m6end macro, and sure enough, it has a bunch of code that seemed to be for checking the SafeZ clearance. The old .020 m6end was actually empty. A bunch of REM statements, and it works just fine, at least for me! I am sure it could cause some Safe Z problems, but I run all my tools with preset Z values and it has always worked in the past.
I will be doing some learning of how to write the scripts when I finally get my tool changer set up in the future, but for now it at least works and makes chips.
Just something you might check.
Jim