So just for my understanding please:
You are using mapextractor and want to extract the "maps" folder from your world of warcraft client, right?
Check if you are really using "mapextractor" and not "vmap4assembler" ore "vmap4extractor".. Run it with sudo rights (on windows -> Run as admin)... Check, that the Folder does not exist, before extracting and if that all does not help you can try editing the worldserver.conf and use the DataPath in order to specify a path for your maps. If that also doesn't works you'll unfortunately have to download an other client.