The entire matter crashed and burned. I left Cairo and ended up two months later in Ghana. But, I never was given any adequate explanation why the visa was not issued. I suspect I now know why, courtesy of the recent Wikileaks dump.
This is from The Atlantic in the context of Libya’s agreement to abandon its nuclear ambitions:
Libya agreed to remove its weapons-grade materials and equipment shortly after a 2003 incident in which the U.S. government intercepted a ship bound for that country with Pakistani-made black-market centrifuges. For six years, Libyan officials complied with U.S.-led international efforts to dismantle the program. In November of last year, when officials without notice halted the dismantling process, the Libyans were down to their last 5.2 kilograms--not enough to make a conventional weapon, but sufficient for a dirty bomb.* A few days later, the U.S. embassy was contacted by Saif al-Islam al-Qaddafi. The son of Muammar al-Qaddafi, Saif is widely seen as Libya's great hope for reform should he win out against his more conservative brother, Mutassim, and succeed their father. But on that day, Saif told the U.S. ambassador to Libya that he was "fed up" with the U.S. (emphasis mine)Now, I can’t be sure that my visa was denied because of the US passport – but the timing of incident is a little more than coincidental. And anyway, it satisfies my curiosity as to what happened.