Ok, somehow I PO'ed many named members of the Great Khans. BUT! I didn't kill a Khan (that I know of.) I have...

Have an "Idolized" Reputation with the Khans.

Completeded all 4 DLCs.

Have an "Idolized" reputation with the NCR

Anyone have any idea what bug hit me? Also, after I completed the four DLCs, I noticed that my "reputation" screen has had... less entries than it had before, as if I never contacted many of the factions. I also noticed that I had red markers in the Great Khan camp (denoting hostiles) and my rep seemed to have (briefly) been set to Neutral with them after completing all four DLCs. The Reputation screen is all fine now, however...