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Where is the problem occurring? If the metadata wasn't there to before the books got to Calibre, then Calibre isn't the problem. If it was there, did it get stripped going into Calibre or in the transfer to the Kindle? You might try manually moving a few titles and see if there's a difference.
I've got a few epubs that I converted to Kindle, never had a problem. I haven't done it recently, though.
If the problem is in Calibre, you'd be more likely to get better assistance by scrolling down to the Calibre hangout.
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