Oh no! Okay I think the problem was that I didn't bother to check the stylesheets of the newer layers to make sure that they were the same as basic boxes green (http://www.dreamwidth.org/customize/advanced/layersource.bml?id=14985). Now that I'm aware of that, it's easy enough to fix.

http://bugs.dwscoalition.org/show_bug.cgi?id=1729, with patch (Tested quickly, and I think that makes it work the way you described. If that looks okay to you, can you review+? That will let me commit. )

Any idea if there's anything else that needs redoing?