@Malcolm: I just came across a similar problem with non-standard MOBI/PRC/AZW files. If you are unable to set metadata on a given file, try clicking 'Convert E-Book' and select MOBI as both the Input and Output format. Then, try exporting the file to your Kindle again, and I think you'll find that the metadata is written correctly.
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Now there is some slight problem with PRC's. That is if a conversion leaves one with both the PRC and the new mobi then the calibre library. looks fine but the Kindle device still screws up (That's a scientific term!) the author and in many cases the title. Removing the mobi and only allowing the PRC file fixes that.
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If I understand you correctly, calibre keeps only one copy of MOBI/PRC/AZW as the MOBI format, but the Kindle allows all of them to co-exist, so you have do some manual file management on the Kindle side. Is that correct?
If so, I'd suggest you upload from the Kindle to calibre, then delete the original on the Kindle. From that point forward, let calibre manage the contents of the Kindle.
G