I know little or nothing about the strange workings of 406 windows but it occurs to me that my driver's window often behaved like that, from time to time, and always had to be 'reprogrammed' by raising it to the fully closed position and holding the switch 'on' for some five seconds. Recently the motor packed up and, after changing it, my garage mechanic was very concerned because it would only move upwards in short bursts and he didn't know why. However, I held the switch down, as described above, and sure enough it has been perfectly all right ever since.
However, this seems such a simple and well known solution that I am sure you will already have tried it, but I offer it just in case!
Eric