I've never seen this behavior - you're not pushing the "Download..." button, I presume... Did the dialog always behave this way, or did it happen after a certain (or uncertain?) event? If the latter, I would try using the "Reset..." button in the dialog and/or gconftool-2 to clear all of your Maemo Mapper settings.. (If the dialog has always duplicated, then this won't have any effect.) Weird indeed. Did your repo settings get changed during one of the duplication bouts you mentioned earlier? Are you able to fix the problem by tweaking the repo's settings?
Use the "Manage Maps" dialog, which allows you to download or delete maps for your current repository. See the Help file for more details.