I am not a native English speaker/writer as you can see/read easily and therefore I am not quite sure if I understand you correctly...
No, I did not load any gcode in between. I started S3D new, loaded the stl and prepared the print with the stored 2 bottom layers and see in the preview mode again 4 green solid layers. If I go back to the prepare view and change the perimeters (without saving) I see them after in the preview mode correctly adapted.
You're not going to like this......but there's no software bug!
Now I see what your model is, its 100% crystal clear there is absolutely nothing wrong with the software! Your model is essentially a rectangular bowl....and the floor of the bowl is approx. 1.2mm thick. And when the model is sliced, the MAXIMUM number of layers possible is four. Set your Top Solid layers to 2 and your Bottom Solid Layers to 2.....and there's your 4 layers. Any value higher than 2....and the additional layers CANNOT be laid down, so they aren't.
If you change both Top and Bottom Solid layers to 1 and look at the preview....there's a gap - of 2 layers!
Result....no bug! This is commonly known in the software industry as "User error".