I'd check that your software isn't doing something similar to Simplify3D (italics added):

"To do this, Simplify3D allows you to specify how many solid layers you want on the top and bottom of your part. For example, if you were printing a simple cube with 5 top and bottom solid layers, the software would print 5 completely solid layers at the top and bottom of the print, but everything else in the middle would be printed as a partially hollow layer. This technique can save a tremendous amount of plastic and time, while still creating very strong parts thanks to Simplify3D’s great infill options. However, depending on what settings you are using, you may notice that the top solid layers of your print are not completely solid. You may see gaps or holes between the extrusions that make up these solid layers. If you have encountered this issue, here are several simple settings that you can adjust to fix it."