I'm puzzled why the ticks aren't in the checkboxes. I've been experimenting and the only way I can remove them in my iTunes is to select the track(s), right click and choose 'uncheck selection'.
You are keeping all your albums in the same location on your PC i.e. not moving them to a different folder after copying to the iPhone?
I've found a couple of settings in Edit, Preferences, Advanced tab for 'Keep iTunes music folder organized' and 'Copy files to iTunes Folder when adding to library'. They're both ticked on mine although the second option shouldn't make a difference and as far as I can see duplicates the albums.
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