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