Both before SP1 and after Pisa and Naples runways are 75% covered in what looks like sand.I haven't had time yet to look at other Italian airports but surely this is a bug in that the runways are too low.Anyone else had this?

That's strange. I've used Capodichino numerous times and don't see any sand. Matter of fact, I just used it yesterday immediately after installing SP1. Can you post a screenshot? Maybe I'm not clear on what you're seeing but the runway looks normal to me.