Hmm not sure what is going on.
We are working on an some sort of memory or buffer issue where the machine become very jerky after running for a while. You may want to try rerunning the same gcode again (you don’t need to put the router in the sled) and see if it seems like the same problems crop up around the same time. If they do, then this is likely the same issue. You can see the discussion here:
http://forums.maslowcnc.com/t/z-axis-not-fully-retracting-before-moving/175/38
The title may be a bit misleading.
If that isn’t your issue, I don’t have any idea.