Solved, with help from Jetguy.
I started jiggling some wires and it turns out that when I jiggle the stepper motor cable, I get the jogs.
I will contact Support.
Here are some pics...
The XY stepper motors have started producing random jogs
that result in the layers being offset and the prints failing. This happens on STLs that printed previously
with no problem so I don't think the problem is with the STL.
This is happening with MakerWare 1.1.1.9 and firmware 6.2 and 7.0.
The glitching can be seen in the red boxes in the image below.
When I make South to North lines there is no problem.
SE to NW lines show the problem.
SW to NE lines are fine.