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I've successfully synced over a 1000 books with a PC and card reader. I honestly dont' think it matters, I've tried both and gotten corruption with both methods and success with both. I personally seem to think it's better to leave the card in the reader, as there seems to be some kind of "Wake up" when the card is inserted and I wonder it that helps with the corruption. Another trick I've tried is to defrag the memorycard before each insertion but that's not foolproof either. You should be able to get 1000 books on there, try 500 at first run, then increments of 100.
From my experience, it doesn't seem to be a hard number limit but perhaps size and time. The longer the Sony has to parse the card, the better the chances of it not getting it all are, so try moving your biggest files over first, etc. Good luck.
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