Hood,
It took a bit of dinking around with the macros and the A has to home pretty slowly in order to be repeatable, but I got everything working and ran a workout program in an endless loop for about an hour. So far, so good.
FWIW, Mach has a bug in it where it will occationally refuse to run a macro . . or maybe it just does not like MY macros . . .

I used M950 for my 'unswap and home' macro. Sometimes Mach will just get stubborn and it goes past the macro but does not execute the code. Close Mach and reopen it and it's fine again. That's not good from a reliability standpoint, however, so far if I just start Mach and load and run a program with the macro in it, everything goes well.
MechanoMan,
I'm having a hard time seeing the purpose of using the 360 rollover if the objective is to have continuous rotation. It's your call, but in my opinion, you are just making a lot more work for yourself using a mode that seems unsuitable for your application. It seems to me that I saw a 'radius compensation' or similar parameter associated with rotary axis, but I haven't had time to go back and research it. The software obviously needs to know how big your part is in order to calculate meaningful feed rates on the A axis circumference. I had no trouble using repeating decimals for steps. Lastly, I do know there are math problems within Mach evidence by a rather severe sidestep at arc tangents when using tool comp. In my example .008 caused a significant side step, yet .009 was perfect.
My comment on computers was general and not directed at your particular issue. I will add, however, that if you are doing all of your trouble shooting on the same computer, assumming your stalls have nothing to do with the computer, you are mistaken. There are numerous examples on this forum of people changing computers and starting to have trouble or of changing computers and their problem disappears. I recently changed from an old dual 850mhz P3 server running Win2k to a Pentuim 1.6ghz running XP. The 'better' computer had constant lock-ups with Mach and all of the motors were stalling like crazy. That computer runs everythig else fine and has for years. It just doesn't like Mach AT ALL! I'm back now on the old server, but I can't use the XBox controller unless I have XP, so . . .