Hi Kevin,
Your printing too fast and your extruder cannot keep up.
Your printing at 5mm³/Sec and many of our UM2 machines top out at less than that.
Try printing finer/slower/hotter until you find the optimum.
This thread should interest you:
http://umforum.ultimaker.com/index.php?/topic/3976-almost-always-missing-layers-underextruding/
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Dim3nsioneer 558
Have you already tried to increase the hot-end temperature a bit? It will make life easier for your printer to melt 2.5 times as much plastics as for the 0.1mm layer height print.
You may also want to have a closer look at the extruder while it is printing the .25mm-layers. Make sure the motor doesn't skip steps and the knurled bolt doesn't slip while transporting the filament.
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