I never used to have this problem at all, but recently (with 1.3b2), whenever I Synchronize a large directory containing many PDFs and images, I get failures in the Log for many of them. If I simply re-synchronize again, some of the failures go away. And if I just keep resynchronizing, ultimately they all go away and I get the files indexed. This has also happened with importing, where drag-and-drop of a PDF keeps saying that the import failed, but I am able to index it, or to import it using File | Import.
John