This is probably a bug, or perhaps I don't understand how the 'screen'
thing for layers works :)

First, make a black (or whatever) backgroundlayer.
Say you have 2 transparant layers (on top of that). On one layers a draw a
line, and on the other layer as well, so they form an X together.
Then I select 'screen' for the upper layer, which still leaves me with an X
but where the lines cross it's a bit more bright.

Now. When you go image->flatten image, the endresult is 1 layer with the
correct image. BUT!, if
a) You use merge down on one of he layers, the upper transparant layer
disappears.
b) you remove or make invisible the black layer, the upper layer disappears
as well.

Here is an XCF file which demonstrates it. Try to merge down the upper
layer, and (undo) and flatten the image. The result should be the same but
isn't.

http://users.skynet?.be/xterm/xterm/bug.xcf