Was dealing with the exact same problem & I can verify that I had multiple copies of the same music files. However, I think I figured it out.
I had originally used Media Manager to copy/sync playlists to my Curve. Those files were stored in a "music" folder on the root of my SD card which I had created.
When I upgraded the BB Desktop software, I opted for Media Sync over Media Manager. What appears to happen is that when you use Media Sync it stores the files in the "blackberry, music, media sync" folder on the SD card along w/ the playlist files.
The original files under my "music" folder still remain. Since the BB Media Player looks for all valid media in the location set in the options (SD card in this example) it finds the files in both locations. What is really aggravating about this is that I store my homemade ringtones in a ringtone folder on the card & it included these in the music list too.
So what I did is, using Windows Explorer I deleted all the "music" in the music folder, leaving the files in the "media sync" folder & presto, no more duplicates. I haven't yet tested this over multiply syncs, so who knows....
Hope this helps...