Hello,my friend's Polo 1.4 SE Mk 5 W reg has exactly the same problem.
Can both your windows be operated by the key in the door barrel method? Her windows can be opened and closed this way.
I'm currently trying to find a second-hand switch unit to see if that's the problem.Only problem is not many Polo's breaking that shape/year.
Let me know how you get on.
SunOnGTiR
June 2009