[-Azrael666-]

That might be your problem. GUEdit doesn't let you overwrite the original map, which in trying to circumvent, you may have done something wrong. You have the original map, then you use GUEdit on it, and save it as the finished map with a different filename. When you go to edit again, you edit the original map, then you re-apply the GUEdit changes to it, and save it, overwriting the finished map. That's how it's supposed to work anyways, I've never edited a map that's had GUEdit applied to it because I always protect them. I have two folders, one for the original maps, one for the finished maps. Make sure you're editing the original map.