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Thanks Kovid.
I've finally got Calibre to transfer all my books to the sony prs-650 without errors and resaonably quickly.
In case anyone else is experiencing a similar problem, here's what I did:
1. Reformatted the reader's main memory (following your suggestion). On the PRS-650 it's under Settings>Initialization>Format Memory>Internal memory
2. Plugged the 650 into the PC and ran error-checking on the main memory (the READER partition).
3. Then tried plugging the 650 into USB socket at the *back* rather than the front (which I had been using up to this point).
4. Fired-up Calibre and got it to manually transfer about 180 books in blocks of 20.
5. Closed Calibre, ejected the 650, and voila - all the books and the collections based on series and tags were present and correct!
Martin
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