It looks like there is z-fighting going on with the light gray building that the smaller rooms are on top of. I almost certain this is the problem. The rule you posted seems to only generate the rooms, and I don't think this rule is the cause of the problem. How did you make the light gray buildings? You could try to either lower the light gray plane of the gray building or raise the elevation of the small rooms by a small amount.
Are the colors incorrect? For example, if one floor is supposed to be blue, is the flickering color blue, or is it a completely different color? (I would like to know if the colors are incorrect because this would be an indication of a bug.)
Note: In your rule, there are still places where you could theoretically get z-fighting. The AddOutline rule ends up creating the floor with the desired color. However, for the rules Lot, Elevator, and StairMaster, it is possible to terminate with some shapes that are not NIL-ed. But, this is not the problem. If you have z-fighting due to the rule, you would see it in CityEngine too. It would also flicker in CityEngine when you move the camera around.
Note: If your Lot rule is executed, then normals would be reversed, but only for the shape that follows the shape tree to Lot. This would not reverse normals for the shapes that proceed through the shape tree to the other rules AddOutline, Report, Elevator, and StairMaster. The important idea I'm trying to say is that when rules are executed, a shape tree is created, and the terminal shapes of the shape tree contain the geometry that you see in the viewport. You can use the Model Hierarchy to visualize the shape tree (Window -> Show Model Hierarchy -> Inspect Model -> click on model).
Rule Application
Standard Rule
Working with the Model Hierarchy Explorer