Originally Posted by rstoothoff
If KDP has a problem with some Calibre-generated .mobi files, but not others, then I should think this is a issue which the developers of Calibre ought to address.
MOBI is a format that is owned by Amazon. They're the only ones with information about how the format works and how to produce proper files. They don't share this information. As you've found they also don't share why they reject some MOBI files produced by calibre.
The only reason calibre can produce MOBI (and Amazon's other formats) files is due to reverse engineering. Only so much can be done by this method. Something will pretty much always be missed. It's even harder when no only is there is a closed service and review process involved.
Not to mention that Amazon has intentionally made changes to their software explicitly to break third party tools. They've done this multiple times and this is why I personally no longer do anything with Amazon formats or devices within calibre. If Amazon doesn't want calibre to work with them then I'm not going to waste time in a battle I'll never win. That said there are other calibre devs who still work on Amazon things. If you can get some reason about why KDP doesn't like I'm sure they will quickly make whatever changes are necessary to satisfy KDP.