Andrew at autolink said it would be the rain rail. so I pulled the carpet back and poured a bucket of water on the roof, water dripped through the rail into the boot in a great load. Oh dear. So rain rail was cleared in June last year when Peter Jones put new roof on. Guess its blocked now. Might visit peter and see if he can unblock it.[:D]
Check the hood is actually inside the rain rail, water needs to be captured inside the rail (like a gutter). If not, there are a series of bolts you can undo all the way round the bottom of the hood, releasing the 3 metal channels holding the base of the hood.
If the hood has been changed the rain rail may have cracks in, it is very brittle. I repaired mine with copious amounts of gaffa tape.
Peter Jones at mazmania replaced myhood and taped up my rain rail as it had cracks and he made sure it was tight. I am trying to arrange to visit him so he can have a look for me.
Saw peter, its a new rain rail £130 next time I go. Oh well the car is 15 years old - what did I expect?