Well...I've been using a single sheet on my truck to keep the sun out. I have it on the outside and it's kind of a pain to put it on since it's so lightweight. I did notice the one time I sprayed the truck down with water that the aluminum sorta melted away where the water contacted it along with the glass so I have clear spots in the sheet, too. Maybe some condensation is what happened to the piece you put in yer skylight? Is the piece you installed have the metal grid in it?
As far as putting it on the roof...I think the weather would beat up pretty bad in short order...since I'm here in Houston. Hurricane, tropical storms, and a daily deluge of wind/rain would probably shred it as soon as I got off the roof. Besides...I currently live in an Home Owners Association (HOA) and they would probably kill the idea before I even got out the ladder.