There is also the theory of one British flight engineer:

According to this, the steering of the planes was perhaps taken out of the pilots' hands, from outside.

The Americans had developed a method in the 1970s, whereby they could rescue hijacked planes by intervening into the computer piloting [automatic pilot system]. This theory says, this technique was abused in this case. That's a theory....

Andreas Von Buelow

http://www.ratical.org/ratville/CAH/VonBuelow.html