I've come across the same problem as oblox — most EPUBs converted to dual-MOBI will result in an AZW3 being sent to my Kindle, but every now and then, my Kindle receives a MOBI.
I believe there is something in the formatting of some dual-MOBIs that is causing Amazon to reject the AZW3 part. When I transfer the exact same dual-MOBI file directly to my Kindle via USB, it will open the AZW3 part. But when I use Send-to-Kindle, Amazon's processing rejects the AZW3 part and I end up with MOBI only.
I have done Send-to-Kindle via email and Send-to-Kindle Mac app and specified my Kindle Voyage. If I skip Send-to-Kindle and transfer the exact same dual-MOBI file directly to my Kindle Voyage, it will open the AZW3 portion just fine, so the problem is occurring in Amazon's processing.
Looking inside the original EPUB (which validates), I saw that the paragraphs were formatted as <div> rather than <p>. I thought aha! that's the problem. But when I changed all the <div> to <p> the problem remained. I'm wondering if there's something in the OPF or html heads that's triggering this problem? I'm just not sure where to look, but am intensely curious to solve this puzzle.