I have [PDOC] as the Personal Doc tag in Preferences -> Output Options -> MOBI Output, but my Calibre-created MOBIs always show up in Books on the Fire (and so presumably do not have PDOC set). This is what I want, but was never sure why this happens until searching the Forums just now.
I always use Bulk Convert (and I start from ePubs that were previously created with the command line ebook-convert, more often than not from a MOBI), and itimpi says this probably turns off PDOC in
PDOC tag different for bulk and individual. So are you using Bulk convert? If so, try Convert individually or try unchecking Use saved conversion settings under Bulk convert.