Make sure you are using Custom Module layouts and Custom Emulators Layouts. I too had this issue awhile back which I posted about. Now I got all those issues fixed but for the life of me I can't remeber if I'm missing something for you also to try. I found that for awhile that if I had too many layouts it would crash, but I believe Ben fixed that problem as I haven't had an issue since working on my theme. If I happen to remember I will let you know. Give that a shot if you haven't already