You're right that it might be due to the albums on your iPod not being on your hard drive. The way the scrobbler works, from my understanding, is that when you plug it in, it checks the play count (of your hard drive's library) for new plays and submits those to last.fm. If no new plays are showing, nothing gets submitted.
When I used to manage my iPod manually, which was over a year ago, I used iSproggler. I'd look into that.
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