I like this topic a lot. Imagine if blur hadn't posted in it. I can imagine the discussion...

Do you have any trigger scenery in layer 4? If so, do you have any animated tiles in the background layers?
You say that the layers disappear in your levels. How about the levels of people that you download?
Do you have other versions of JJ2? Can they view your layers?
Are you using a Jazz2.exe that you downloaded from somewhere?
What version is your JJ2? Is it a 1.00 version?

Eventually, n00b would fix the problem by himself, and by that time we would have constructed a very elaborate theory which was completely wrong. JCS gets my vote for coolest forum.