There's nothing wrong with Lion. Issue is that jD is a complete mess when it comes to reliability of file operations. jD not only has issue with writing files but has an issue with losing files during a rename. I've reported that issue long time ago and jD still loses files even though the thread is marked as [Solved].
Quit trying to pass the buck onto the OS... no other app has these severe file issues that jD has.
I've moved away from jD and now use it only rarely. I just can't trust it at all.
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