Hi,
Had this problem 15 yrs ago when I built my house, patio door in gable was covered in marks, some like raindrops others like streak of water. Sad news is they couldn't be removed, explanation I got was that they were marks from where it probably rained after gable was plastered and the little splashes of plastery water stain the glass because cement contains some sort of acid and it actually etches the glass causing a permanent mark. Fast forward to 4 yrs ago when I built a sun room onto same gable, was able to get rid of patio door, because obviously there was going to be a lot of glass in this sun room I explained previous problem to the builder and told him I wanted the windows covered with plastic before plastering. He rubbished previous explanation I had been given and said there was not need to cover windows, he said he would get plasterer to clean windows immediately after plastering (it was dry weather so rain wasnt a problem). Anyway plasterer did clean windows straight after plastering but unfortunately cleaning windows with sponge and bucket of water which gets all gritty from plaster splashes didnt do windows much good either and I still got some of the same etched marks on the windows plus scratches from the grit. Very annoying especially in sun room as when sun shines through the windows it is very obvious, one of the windows had to be replaced by the window company because seal went and the difference between that clear new window and the existing ones just makes it worse. If I was building anything again I would cover the glass with plastic myself to protect it. Sorry cant give you any good news!