It may take 9 seconds but do the windows end up in the correct place.
I have A3 Cabrio, idenitified the problem to Audi garage at begining of August and audi have only just admitted its a known software fault. The rear windows do not come to rest in the same position once the hood is open or closed for that matter. Took a little time to get the Audi garage to contact audi about it.... fault what fault.
I have yet to get a date from them when this will be fixed and concerned they are not passing this onto the dealers to report to customers.