I'm seeing a similar problem (Windows XP, Calibre 0.7.1, Sony PRS-700).
Any time I do anything with the device (add a book, delete a book, update an author name, whatever) the actual update happens very fast, but 'sending metadata' always takes just over a minute. Over and over I have two entries in the job log. The first shows the book delete taking 0m 0s. The second shows sending metadata for 1m 4s or thereabouts. Its always just over a minute. Makes me wonder if there's a 60 second timeout involved somehow.
(Collections: 116, Books 762)