Quote:

I mean the clock on the airplane could be slower because its pretty cold up there, and the colder it is the slower things go.



Quote:

Couldnt it be that the one clock had a little malfunction? Maybe because of the flight and g-forces?



No (on both accounts). The clock used was an atomic clock. Here is some information on atomic clocks:

http://science.howstuffworks.com/atomic-clock1.htm

http://en.wikipedia.org/wiki/Atomic_clock

The nature of an atomic clock is what would have caused Professor Alley to choose them for his experiment.

Professional 2D, 3D and Real-Time 3D Content Creation:
HyperGraph Studios