Hi Mike welcome to the forum sounds like you found this forum the way i did because your having troubles with your Eos.
Well I too had a leaky roof, open the boot and looked at the spare wheel and theres a 1inch pool of water. (this becomes a long story) but the outcome is that the dealership couldnt fix it the eggheads from VW couldnt fix it so I asked for my money back and started to look at alternative cars.
truth be known we couldnt see anything which compared so instead we asked for a new car same spec to which they have agreed and I am now awaiting my new Eos.
But while were waiting I asked for my eos back saying I would drain the boot once a week which I am doing. but and this is a big but I have now got the most squeaky roof ever. (dont know whether this has been caused by all the work and seal changing thats been done) but if Im honest though I havent tried Krytox to fix the squeak problem.
hope you get a good outcome quickly.