That's happened to me too, when I tried to make an alternate warp into Brock's gym...
I tried a few things, but I am clueless as to what causes it (I think it's something about entering a building from a custom map). I recommend using cntrl+right click to just select the whole map and paste it onto a new map, then insert that map somewhere else. That worked out pretty well for me.
EDIT: Darn it all, someone else answered while I was typing. Ah well. It's basically the same solution, only his is simpler.
To my would-be helpers...
Thanks for the enthusiastic file-sharing recommendations, but for now, does either of you know why my maps keep getting compressed to the left like that? For anyone else who sees this post, basically I'm trying to insert a world map, but it just turns into two long lines of crud on unLZ. Also, if anyone could shoot me a link to a world-map tutorial other than haefele's, that would be great. There used to be several, I think, but for some reason they're gone now...