Hi Shannon,
Yikes! When you say 1 of 20 Jobs - how long are the jobs? What do they mainly consist of? Long paths with short vectors? Any Rapids? What level of Look Ahead Time are you using? If you leave KMotion.exe open are there any messages on the Console Screen? Can you re-create the problem with a simple job? Please post your configuration parameters.
It sounds like something is getting corrupted. Can you try a Step Response Plot after having the problem and re-initializing? That might give some clues on what is still working and what is not. For example is the trajectory (blue plot) looking normal? Is the servo Output (green) Normal? Encoder Reading (red) reasonable?
Another approach is to capture the motion trajectory with a C program with a circular buffer and if you can somehow trigger on something going wrong (axis disabled, sudden z change, etc), that might provide some clues. I've attached a Capture program that will capture data and trigger on a z (chan2) following error of more than 20 counts and will then write 1000 data samples to a file. Mostly before the trigger and 20 samples after the trigger.
Regards