Since Calibre has bug reporting tools, all Amazon has to do is explain what needs to be changed in Calibre's MOBI headers and they would likely get fixed.
I don't see the point of DRM on ebooks submitted via DTP, which are likely to be bargain priced and therefore relatively piracy resistant. If you have to include DRM, I would try HTML -> MOBI (Calibre); MOBI -> ePub (Calibre again); ePub to AZW/MOBI (kindlegen). This is a bit simpler than DiapDealer's work flow referenced by ldolse, assuming it works (which it might not).
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