ITunes doesn't seem to know how to count,  multiple references for same mp3

Have had several MP3 players, but just got my first ipod.
I have 5899 mp3 files under the My Music directory stucture.
The two other programs I use to manage my music (Rio Music Manager, and Media Monkey) both see 5899 songs and one copy of each file.
Also a directory from the CMD prompt verifies 5899 mp3 files.. totalling about 24GB
When iTunes scans the same directory it shows 10,352 songs or a total of 38.79GB.
I should be able to put my entire collection on the 30GB video ipod, but because of what itunes is doing, they do not fit.
I see most all songs with 2-3 references in the library. I have to uncheck 2 of the three to have iTunes only send one copy to the player..
I have uninstalled iTunes twice and it does the same thing every time..
Love the ipod, but iTunes needs help..
Any ideas?
TIA,
Bryan
IBM T43   Windows XP Pro  

actually think I found my own answer. I have 5 M3U playlists under the directory structure. Synch lists and playlists for my other players..
I moved them out, then cleared the itunes database, rescanned the directories and only 5899 songs came in..
Any way to bring my m3u lists in without the dupication?
Bryan

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