I have an angled upper corner cabinet with two doors, upper and lower, the upper door maintains it's size with the proper overlays but the lower door does not. When I add the door it correctly sizes it but when I go to the main area from the door area the overlays vanish and the door resizes itself.
This is a bug and I have passed it along to the programmers. This is something you could try for a work around. Add a bottom rail that has a width of .125 to the bottom opening then change your bottom overlap to 0 when you re add the bottom door. Hope this works for you and sorry for the inconvenience.