This happened to me as well and it was because I had Windows Media Center set as my default (as well as auto converting all files into .wma) so itunes automatically converts all .wma files and the original .mp3 files when it moves them into itunes. It sees each file as a different song. You'll have to delete all your .wma files to that future itune imports won't do this again and then go into itunes and do a search function and manually delete all duplicates. Or store your backups on a completely different HD.

Also disable Windows as your default and go into Windows and uncheck the box that says auto convert to .wma, just leave everything in .mp3 and let itunes deal with the rest.

This is all assuming you have Windows. If you have a Mac, you probably still have multiple file formats of the same song stored somewhere (I'm not sure where exactly) and you'll have to find those and delete them or move them into another HD completely so itunes doesn't "see" 2.