Hi guys. Thank you very much!
Phase,
I agree with Hood - I think you have a problem with the driver recognition of the direction signal for your Y Axis. Perhaps a thorough check of your connections PC to BoB to Drivers etc may reveal the problem.
Tweakie.
Stepper motors can turn the wrong direction when one lead to one coil is broken. The motor will also run very rough.
It seems that the first step is to check the connections of the Y-axis and the LPT cable. It kind of makes sense that it would recover randomly and then lose it again once the vibrations of the cutting start. However, it does not quite jive with my recollection that the Mach display and the table both only increment. You would expect the Mach display to increment and decrement correctly (independently) if the problem is down the line from the software... but I could be remembering it wrong so it is worth a shot

I have heard of this issue with some of the hacked versions of Mach, another possibility could be bad wiring on the Direction signal for that axis, sometimes it makes others it doesnt.
Hood
That could be also a factor. I have the licensed software, but it is a version that is now a couple of years old. Weird that it would have worked fine for a while and then crap up though. If the checking of the cables does not work I'll reapply the XP optimization (in case things somehow changed).
It that does not work then I'll swap in a new hard drive and rebuild the system installing the newest version of Mach. The pain with that is all the configuration and also that I have applied a path to zero the tool and I'm not even sure where I got it from

Today I'm swamped working on taxes. Will post an update tomorrow or Thursday as I get some time to work on it.
Thanks!!!