I ripped my CD collection to my PC, then copied it to a 4th Gen 40 GB iPod.
Sometimes I listen to the music on the iPod; other times, on the PC with iTunes.
But each time I listen to a song -- either on the iPod or on the PC -- a new "Last Played" date gets assigned to the song file.
So the same song can have different "last played" dates, depending on when it was last played on the iPod or PC.
Because of this, iTunes treats the same song file as two different files, and ends up duplicating a lot of music files on the iPod -- thus taking up unnecessary space.
FWIW, I use "manual update" to the iPod, not Automatic.
Don't know of any program specific, but
There are programs avilable to scrub (or replace) file attribute fields in bulk.
So, manually scrubbing the pc hdd files of the last played field before transfers to IPod could do the trick.
Also
I think ITunes has a "search for duplicates" option in it. I know that fixed a similar problem I had.