Roof leak through Thule air-con unit

[AlunandFelicie]

At a festival over the weekend we started to get water dripping through the unit(not in use) we were fairly close to level on chocks ,checking the instructions Thule say not to use silicone to seal the roof but to contact them(presumably so they can sell me a new rubber seal).
anyone had a similar problem and a ready remedy?
cheers