Is it the same pin? I don't think that would be a problem. I just looked at my (working) VGA cord and it's missing one on one end. Are you sure you have all your display settings on your computer correct?
EDIT: I didn't even realize that I have a VGA extension.... I said one end was missing a pin, but it was really both ends of one cord, the other cord has all pins... and together they are fully functional. It is one of the pins in the middle row one away from one of the sides, right?
EDIT 2: Wrong again... both cords are missing one pin. I have a Male-female from my TV which is missing one pin on the male side... then a Male-Male extension which has 15 on one side, and 14 on the other. This all goes to a mini DVI. It's got to be your computer settings.