Only advice I can offer is try resetting the windows again, do they go up when they're down as you hold the fob still? My wind deflectors caused an issue with the anti trap and although you couldn't tell anything was wrong I slowly worked it out and it was the wind deflectors causing trouble. Since I have used number plate tape cut thinly to make sure they're cemented in both front and back. I would say try putting your windows up with the key, that should indicate whether it's the key or car. Also, try resetting your head unit back to factory settings.
Cheers, will try those tomorrow and let you know how I get on!