I've got the same problem in my 2.8 Quattro - £38k top of the range car when it was new with manual rear windows! Nice one Audi.
Someone on here suggested manual rear windows were a "no charge" de-option i.e. you could specify manual over the standard electric at no extra charge (or maybe get something else cheaper, like cc in lieu of sunroof), though why anyone would do this is beyond me. My car doesn't have any other options anyway apart from leather and I doubt even Audi would have cheaper leather in lieu of electric rears.