Hmmm... Ya, is it in grey scale?
If it isn't it doesn't work. That's the only problem I can think of. I make Alot of maps...so yes I've messed up some and that's the only reason I think it could be a problem...
If so here's how to fix it
1. Go to gimp
2. Open files
3. Pick your map terrain
4. Click new page (DO NOT EXIT OUT OF FIRST ONE)
5. On new page MAKE SURE YOU HAVE grayscale!!
6. Paste
7. On docuable diologs get out layers
8. Ancore down Layers and save
Sorry for it not being very discripted...not on gimp ATM, on iPod. This is how I fixed it. If you didn't understand just PM me and I'll get back to you as soon as i can.