Leaking Prado Roof Rack

Hi,
(2003 Prado 120 series) Just had the roof repaired, took off the Toyota rack supports and the internal lining and found that the holes have been leaking inside. Not a lot but constant dripping. Hence the rust around the mounting hardware inside.
It seems that a) the bolts were not put on tightly b) the O-rings sealing the bolt hole went hard and c) there seems to be a plate missing from under the outside support plate and its associated O-ring.
My Toyota racks go across the roof (3).
Has anyone else found the rack mounts to be a problem? There seems to be a design problem as the water collects around the support bar in the roof channel. Not to mention the grass, sand, mud and other vegie bits!

Bill