My experience with iTunes for Mac is that if you import as you are doing in the image above, track 6 already exists in the iTunes database. iTunes does not check if it exists in the media folder, only its database.
Also, if the track 6 is not in the database but track 7 or other higher-numbered tracks are it will not ask to replace and will instead rip an extra track.
I'm not sure about the empty/unplayable tracks,but check your database first, expecially if you delete tracks through the media folder and not from the iTunes database. Especially if you've set iTunes to automatically manage your tracks, you should be managing tracks from iTunes. If you do things in the OS that aren't reflected in iTunes, its behavior will be erratic. If you want to work on tracks outside of iTunes, remove them from iTunes without deleting, modify them, then reimport.
Give it a shot and if doesn't work you might want to post a new thread in the iTunes for Windows community, as it should get more attention in a new thread.