Has anyone seen this?  This happens after cutting for a while.  I load a new gcode file, from the same model and when I hit start cycle, it doesn't start.  It might move down one or two lines, I'm not real sure about that, but it must be sending code to the buffer, because it looses its place and is hard to restart without re zeroing everything.  I'm new to cnc, so I'm not the best at troubleshooting, but I don't think it is noise in the lines or snything like that since it always only happens at the start of a cycle.  Maybe the controller is overheating?  It's a Gecko 540.  Any advice would be appreciated. 
Thanks

I think your starting location has not being defined.
Move x y and z to the starting location. Zero X and Y and Z.
Now Start Cycle.

A lot of Gcodes files send positive values of z axis. If your z is not zeroed on the material surface, z0 would be at the top and the program cannot start because z>0 would exceed  the axis limit of the machine.