There is an option in the Terrain Editor (The main-part of the World Editor where you can view the map terraining etc). I can't remember correctly but I think it's where you can choose "save, save as, Open etc." Something like Prefecences or something, here you can find a checkbox that says "Allow negative values", just check that one (Sorry if I'm not clear anough, havent got access to WE myself at this point so I can't be any more specific).
Ghan has said he has fixed this. Monovertex please confirm this fix. This was only a problem with people that had signatures in the upper levels like not the special members but the respected members.