I am having a similar problem, however, I am thinking that it is the noise (electrical) from my lousy (Harbor Freight) router. I never get the hiccups when dry running and not having the router motor running. I get e-stops and am told that a limit tripped, but it does not show which tripped, I am convinced that the switches are not tripping as it take about an 1/8th In travel to actuate them and there are no items that would have done so when it trips. The problem seems to only exist when the router is running. Problem can happen within seconds of starting the cuts to 10-15 minutes into the program.
In trying to resolve this problem I went from quick dis-connects at the switches to soldering them. I isolated all AC power, in particular I moved the routers AC to the opposite side of the gantry, all limit switches have shielded cables grounded at the BOB and kept inches or more from the stepper cables from each other. Going to install a new router to see if the crappy one I am using is the problem.
When running a program that increments y about .25" and moves x 32 or so inches then increments y again and moves x in the other direction, some times it would skip 4-6 trips down the board and start somewhere 2-3 inches from where it should have been. Multiple lines of code skipped.
This is a home built CNC router, running win 7 with WiFi, but not running anything else while using machine. As this has been built by myself, I am checking every connection, added a terminal block for the limit switch inputs, made sure the BOB is secure and connections tight.
I will keep you updated if the router is/was the problem
Any thoughts or suggestions would be most appreciated