My theory:

Imagine rendering this. When you are moving away from the runway, the lights positions would apear to move up in the y direction on your screen. This is because you are going up so the distance between the lights on your screen gets bigger (it would be biggest if you are right above the runway). Vice versa for approaching the runway. To envision this better, choose two points on your table (put your fingers there) and now look at it from above and from the side. When looking at it from the side, the distance between the points on the y axis of your viewing plane is 0.

I think our brain sees the light as a different object when it is on or off. While it is on, the light seems to move up on your 'screen', then it goes off ('dissapears') and goes on again: 'reapears' (if it would continue to move 'up' at that speed) at the position of the next light.

Now if the lights would be on all the time we would see this as just the effect of going down but because of the flashing they seem to move away.