MM_Build, Interesting information. I have a MK3 0.5mm nozzle with a cut down tip. It is possible that its not flat. When it extrudes material in the air the stream tends to go to one side.
At 50mm/s, 230 C and after rerunning the 100mm extrusion calibration in skeinpypy, an 8 hour build completed successfully without the holes. Thanks for all the help. Now I have to order more PLA.