Well, I have run into a peculiar issue that needed to be addressed, and all of the things I have done so far in troubleshooting have not produced any fruitful results.  

Description of the issue: 

Every time I try to run the default code that comes up in the axis window, I get a few missed steps on the Y axis that ends up skewing the rest of the cut.  You can see it evidenced here: 

The last 'C' in LinuxCNC is almost ALWAYS the problem, but sometimes it is the first C.  And another of a Harley Logo that I toolpathed using V-carve.  As it engraves the letters MOTOR the m turns out ok, but the O is pulled low, and I'd be lucky if the TOR stays together a little bit lower on the -Y direction.  Get my point?

So first thing I am going to do at this point is reinstall the system.  This may be a latency issue that I can fix using the older version of Ubuntu - Hardy Heron 8.04.  And just manually update emc2 to LinuxCNC 2.6.  Will update the progress.