I've verified everything is programmed correctly and changed the coding to 07006C. I still have the same issue. Every time I test I have to reset the auto up/down on the windows. It doesn't seem to be consistent either. The back windows have always needed reset, but the fronts not all the time. Can this have anything to do with it being a US spec S3? I've seen a thread before where a MK7 user had the same issue, but can not find it now.Not experienced this myself with any of the cars I have done but then I have only ever used VCDS for this function. Are you sure everything has been coded correctly? If your tool has a coding log I would look through it to make sure that no additional / incorrect codings were made by both yourself or the tool.
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