Windows do not lower using the buttons.
What does that mean exactly?
Using the comfort function of the remotes
Using the buttons in the middle console
Do the windows lower "an half inch", when you pull the handles inside or outside?
What model year is your car? (There are some differences concerning the wiring).
Did you check if there was water getting in the "waterproof box"? This would have been my first step.
In general 2 beeps directly after closing means a bad alarm control module.
Also please check, if you have water standing in the doors. Had a customer with a bad windows seal. Water came in through the drivers door.