There's probably one of two reasons:
If it is every track, are you sure you have not got two copies of your music (one in the iPod_control folder and one dragged 'n' dropped, maybe?
Otherwise, you may just have not waited until the initilisation was complete.
Reset all settings, do an 'initialise now' then wait 10-15 mins
Shutdown and restart, then reload your settings. That should do the trick.