Seems there was a story during the Arab Spring where weapons were being shipped overland from Libya in an Iranian convoy and the Israelis caught the convoy in the open, in an East African nation....
This is what I was thinking of but there was no mention of Libya or MANPADS in this particular article:
Israel bombed Iranian convoy in Sudan: report
Tuesday, 31 March 2009
http://www.alarabiya.net/articles/2009/03/31/69614.html
That could account for some, but recall also the photos of fully laden cargo ships. Where did they go? After Operation El Dorado Canyon, Muammar went on a MANPAD buying binge. Almost 3 decades of a plan to put a MANPAD behind every date palm. I don't believe all are accounted for. It would only take a handful to generate a 9/11-level attack.