I suspect that the fault lies in your window switches or the loom attached to them. There is a possibility that the window switches are not receiving input voltage though.
Essentially on the Lupo, as with most Volkswagens, the electric windows are triggered by two different inputs. One is when unlock or lock is held for several seconds, the car sends signals to the motors to open or close. The other is that, when the ignition key is in the accessory power mode (or higher) then pulling or pushing the window switch will send a signal to the motor to raise or lower the window.
You've already proven that there is no problem with the motor so it's reasonable to assume that the problem lies with the switch or the accessory ignition power circuit. I'd remove the loom from the back of the switch and measure input voltage when the key is turned. If voltage is observed then check the resistance across the pins of the window switch when the switch is in both the open and closed positions.
I'd also start checking fuses. I have a hunch that the switches are on the same circuit as the cigarette lighter but I'm not 100% certain on that one.
Finally, if you have access to VCDS / VAG-COM, scan for fault codes. The electric window system is definitely monitored and fault codes available via diagnostics.