Had a similar problem, found this solution on another site: It looks like if you delete one of the files to be sync'ed from your harddrive then the Sony software hangs. In the Library, preview each book that is to be synced and see if any are missing. I found one, and once deleted it from my library, synced fine.
The sad thing is the solution I found was for ver 3.1. I'm using ver 3.3. So obviously 2 minor releases and they haven't fixed such a stupid bug. I do some programming for my company and would be embarrassed about this bug, but would promptly release a new version just for this fix. Sony apparently has no such qualms about ignoring these bugs. I'm going to go check out calibre.
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