I think what you are doing is resuming from the incomplete folder right? Even though you delete files from the download window, there is still a incomplete file in the incomplete folder. That file should also be deleted.

Otherwise, make a note of all your option settings, then try deleting your LW Preferences folder whilst LW is closed; instructions here: Point #2 & 3 in Fixes for Limewire (sample image included at bottom of page.)