Layer issues in line with holes on the Z axis

I recently completed my first 3d printer. It is the Mendelmax 1.5. I'm now trying to use it to print the parts for a second Mendelmax and I am running into some issues whenever there are holes on the vertical axis. Its almost like it is missing layers but if I look at it while it is printing it seems to be hitting the layer but just really under extruding as the infill looks very stringy and incomplete on those layers. The prints are fine on layers that aren't in line with holes. What might be going on here?

(I'm getting an error when attaching an image but I think there is a link below to my flickr account with a picture of the issue.)

have a look at your retraction settings, you might be retracting too much and not putting enough filament through on restart, thats why it looks like under extrusion only after the holes where a retraction would have happened

That sounds reasonable. I'm using Cura and I think that it allows for additional feed after a retraction to compensate for that. Thanks for the diagnosis!

That ended up being the issue. I changed retraction to 1 mm and added an additional .1mm on the other side to re-prime the nozzle after the move. Now the prints are coming out solid. Thanks @scottybfg!