You can see the process I made to make this happen and the results here:
https://youtu.be/Pqa5GElOYbQ?t=8m50s
If you set up multi-processes and change the layer height of each process, it is possible for a gap to appear between layers.
My guess is that the layers are being calculated from the build plate, and not the bottom of the process, and when they don't line up just right there's a chance that the result will be a gap.