Hi i have just purchased a soft top roof for my 3 door landrover, we put the soft top roof on but the back window would not go up, we took it back of and put the hard roof back on and the window was ok.
The soft top should have came with a plastic clear sheet that takes the place of the window.
There is a micro switch that is built into the frame of the car (when you remove the hardback the window drops) I suppose you could over ride this in some fashion, but you would be better to get the correct sheet.