Originally Posted by HarryT
I don't think it's that so much as the fact they're now using a better MobiPocket creation tool.
Baen are much the same; their older Mobi books with a ".prc" extension are rather primitive and lack navigation links, etc. Their more modern Mobi books (with a ".mobi" extension) have proper cover images, working nav links, etc.
Well, the two files look identical other than the cover image, and they both have a prc extension. So if it's not a question of compatibility with older readers, I don't see the point in offering the two options. It's not like they explain what the difference is and why you'd choose one over the other (if they do, I didn't find it).
This very thread says all the older, already purchased books will now be available in the new eReader version (and by the way they list THREE .pdb versions), so clearly it's possible to make the kindle version available for every book (if they're not already doing so).