Dave,
Are you using backlash compensation?
Exact stop or CV mode? Maybe just post the  XML file.
What version of Mach are you using?

I am just attaching a pic of the hinge for others to see that your contouring the hinge and there are a lot of moves ( some of them .005 to .010" ).
With a lot of moves the chance to skip steps goes up and there is a fair amount of change in direction. ( One file has 20000 lines of code compared to 1000 in the other )

I would have thought that since the drive is meant to stop on some range of  / or an error your axis would have stopped moving ( i think that's what i read above......) so that would have given you
some idea on where in the code it happened and provide a way of maybe trying to hone in on the problem.

The problem, the way i see it is it can be the drive control loop or the machine is creating the problem. There are a number of things that you could do, such as:
- Air cut only with all  axes, with the just the X axis, with just the Y axis
- Bypass that controller board if possible. If the stepper is going to skip it will skip with or without some loop
- Place a pause in the code every so often so you can see if the error is cumulative ie; say every 100 lines in the 1000 line code ( G4  P5 gives you 5 seconds to check position )
- Swap the drives and do similar to the first suggestion
- Just write a little subroutine that repeats some of the moves thus is easier to monitor for postion or try to create a repeatable axis fault

Sometimes it's easy and sometimes it's not...........
How do I know ?........... Well i have a similar problem with my mill when running some 3D contouring. I know it's is not the Gcode, nor the drives, nor Mach, don't think it's a setting
 and believe it's machine related. It is a PITA. Since the machine never skipped in years. I have some thoughts on mine, but am not going to muddy this thread up with my problem as i am interested in solving yours.

BTW, Now you don't need to feel like your alone!
RICH