I see. I'll give it a test by this weekend to see what caused the problem.
Let's start from how do you reproduce this problem. I started the test using Galv's master demo and added UT_PreserveMapScene to the plugin list. When I started the game and went to the layered graphics map, opened and closed the menu, every thing seemed fine.
But it appears you are not using the standard UI? I see you have some Hendrix plugins which are related to the menu, maybe I should test with them with layered graphics. But if you have a valid demo it will make my life easier, considering you are using quite a lot of plugins, I need to find and set them up.