I know what you mean, I catch myself doing the same... and not only once. But here... hm?
On all of the layer include exactly that what shoud be on..
Cities - only the few dots.
Roads - The realistic looking roads.
Foreast - The Forest and the shading
Mountains - The Mountains and the shading
Hills - The Hills and the shading
Rivers - my beautiful pink rivers..
Coastline - the first line a drew here..
And last is the background...

The 3 colored areas are already deleted.
Foreast, Hills and Mountains are switched to the multiple mode.

If I hide the Rivers, Coastline and the Background, I cannot see the hills, mountains and the forest. Thats wired.
Only if the background is shown I can see these as well.. But they are not at the background.
really strange -.-

My it be that I've done something wrong with the hills, mnts, forest and with they shaders? Maybe I merged in the wrong direction?
Right:
Forest Shaders -> Foreast
Wrong:
Foreast -> Forest Shaders

?!
Because in you tut you have the ... shaders at the end.
In my try I have the "real layers".

grr, this is pain in the ass!!

#yosh