Ok let me respond a little longer.
This is my answer. And by the way, I'm not a guy in a call center I own a shop that fixes EXCLUSIVELY VW, Audi, BMW, Porsche, Mini, and other supercars (Lotus, etc), I may not have explained it correctly or to your satisfaction, but I'll try. I'm not saying go to the dealer, I'm telling you you must buy the correct tools. Here's the rest of the information. I don't normally go into great depth both because most people get mad when I tell them they don't own the proper tools and then don't hit accept and I don't get paid for one, and two, the electrical theory and info needed to describe what's wrong with your car is over most people's heads.
Your vehicle is equipped with power window motors which sense force so they know if somebody has their hand or head caught in them, it's based upon voltage and amperage that the motor is drawing. When battery voltage gets low, it throws this off. Not only that, but the modules in the car won't go to sleep in the correct manner, this will CAUSE a 1 amp or more draw. So, you must fix the charging system issues or whatever the case is before we even begin to diagnose a draw on the system. That's why I told you to do the test that I did, which CAN be done with the tool you have. Also, a capacitive discharge is nessessary to reset all the capacitors in the vehicle, this requires removing the battery cables and touching them to each other for a few minutes.
After this the windows may function, but also you may need a scan tool to erase faults in the module that controls all of this. That I cannot control.
Your test you are doing is invalid because until your modules have been put to sleep, you cannot test for a parasitic draw. Per factory instructions typical of all German makes, this requires you to arm the alarm and wait up to an hour while watching the amperage spikes. You simply cannot perform this test without an amp clamp. Until you restore the battery to full voltage and then repeat the test as I described, you're chasing your tail.
I got in this same arguement with my step dad trying to fix my mom's x3 about a month ago, this isn't a Chevy or a Ford, it's a Porsche, it doesn't function like anything other than a German car, and without the proper tools and the procedures I have described you CANNOT diagnose the problem. Once you do have an ammeter as I described (which Harbor Freight sells
fairly cheaply) then you can do the test as I've described. So real quick without full explanation again, you must follow the steps as below.
1. Disconnect and FULLY charge battery
2. Touch the negative and positive battery cables together while disconnected for a couple minutes.
3. Reconnect and check operation of windows, if they won't work, buy a scan tool capable of communicating with this vehicle's comfort module.
4. Check charging system operation as described, if that's found to be ok, proceed to step five.
5. Buy an ammeter, open all doors and the hood but latch the latches manually, arm the alarm, wait 30 minutes and check parasitic draw, if there's STILL a draw, then we start looking for the offending module, which may very will be one of the window motors or the module itself.
I never advocated the dealership, they're a waste of money.