Not sure if it's the same problem, but something like this happens with the CSMIO motion controllers when you do a tool-change invoiving a touch-off operation - it just gets confused. Fortunately, the answer in that case is to "upgrade" to a slightly earlier version of Mach3. I'm now running .028 (from memory) and that works absolutely fine. M6 tool-changes with touch-off tool setting aren't a problem.

Not sure if you are seeing the same or closely-related problem, but might be worth looking at. Life is easier if you don't have to switch files!