We had new windows and doors fitted at the end of last year. Cost us a small fortune, and they look perfect in normal sun or cloudy days, but in low sun and first thing in a morning they look terrible......
It's all on the inside of the unit. Dust, and even the odd finger print. Windows aren't as good now as they used to be. The only good thing is that there's no visible seals on new windows which helps minimise run downs.
I'd check first that it is actually a problem with you and not just the inside of the glass.