Amazon May Not Be Taking Calibre Converted Mobi Files
Whilst preparing to turn in a project, I just ran across this article, which says some folks have had problems with Calibre-converted .mobi files with Amazon. I haven't run across this, largely because I now preferentially use kindlegen. As noted at the MobileRead Wiki, this means the resulting file is typically twice as large. For the project in question, that's a 50 MEGABYTE eBook.
So I picked up kindlestrip - a quick little python program to pull out that extra duplicated crap.
Both are command line (though the Kindle Previewer might serve the role of kindlegen for you... might...) programs, but they're easy to use.
python kindlestrip.py [original.mobi] [outputfile.mobi]