try realigning the seal,mastic the top edge behind the plastic moulding above the window, also the roof rails can allow water in where they join the roof, you can spend a few happy hours with a hose pipe identifying the problem, i am sure a search on here will give you more info
might be worth a try to pull the rubber seal off all the way round then refit it. It will go back ever so slightly different, but that may affect a cure.