This should not be happening. Updating play counts, etc. should not cause tracks to appear to re-upload to your iPod. The only time this should happen is if you make a change that effects a track's metadata (change the a track name, change the genre, add/change album artwork, etc.) or if you actually re-rip the track. Changing the metadata actually alters the music file so it must be re-uploaded. Changes to the play count, skip count, ratings, etc. are made only in the iTunes database and do not effect the actual music file.
If you have all of your music on your computer, you can try creating a new blank library (
Click here to see how) and re-adding all of your music to the new library. It is possible that your current library is corrupt. Be certain that you have all of your music in the new library because when you sync the iPod it will completely replace its contents with that of the new library.
You can also try uninstalling iTunes then re-installing it to see of that makes a difference.