Yeah, just beware that 3.043.066 is not without plenty of its own bugs. But at least you've confirmed that the version of Mach3 you were running is the culprit.
You might want to go to the ArtSoft forum, and ask the guys over there which version is best. Most consider 066 to be too buggy to use, but I don't recall which version they feel is most stable. I believe that particular bug was fixed somewhere around 3.042.060 or so.
Probably be good to report the problem to Tormach as well, and send them the problem g-code, so they can reproduce it. Perhaps they're already aware of it, and might have a work-around?
Regards,
Ray L.