The open source ebook tool calibre has been able to make Kindle ebooks for several years now, and for mot of that time Amazon has accepted those ebooks into KDP with scarcely a murmur. While they often looked down their nose at the app, it wasn't until very recently that Amazon decided to start refusing to let authors submit ebooks made with it.
I found thread over on MobileRead that a conversion specialist started earlier this week. The tech reported that one of their customers had a book bounced by Amazon. After first sitting on the ebook for close to a month, Amazon finally gave this explanation:
Our technical team has found that the content of your book was created by 'Calibre', hence it is not buyable on our web site.
Please upload your book in either a MOBI file created by KindleGen or upload the content file in Doc/HTML format. The book will then be made buyable and searchable in the next 24-48 hours after republishing.
Thank you for your immense patience and understanding during the time it took to research this issue.
That's a first, not just for the specialist but for me and pretty much everyone who has submitted ebooks to Amazon. While Amazon doesn't much like the fact we use unapproved tools, they've never gone so far as to refuse them simply because of the tools you used.
In fact, the only times I've heard of Amazon rejecting ebooks (including a retroactive rejection) were due to technical issues in the ebooks like poor image quality, horrendous formatting, and the like. (They also reject ebooks because they're public domain or simply junk, but that's not an issue here.)
And it turns out that in this case calibre probably did introduce some technical issues when the Kindle ebook was made. Another converter responded a few hours later with a similar report as well as a possible cause.
The problem is simpler than I expected. Calibre recently got the ability to make the combined KF8/Mobi ebook files that Amazon really wants you to submit. Unfortunately, it doesn't do a very good job. According to Kovid Goyal, the primary developer of calibre (in reply to another comment):
If you were generating plain old MOBI files then that is highly unlikely as calibre's MOBI output has not had any significant changes in a long time. If you were generating combined MOBI/KF8 then it is possible.
So it seems that Amazon might be rejecting ebooks because of flaws in how they're made. That would be good news, because it means that you can fix and or prevent the problem by simply selecting the correct options while making the ebook.
I'd go back to simply making an ordinary Mobi ebook, at least for now. Leave the KF8 alone until the bugs get worked out of calibre.