To answer your question, I've read that the seals are a common problem with this bike. I've not had any issues with mine in 14K miles, but some do, and others go upwards of 50-70K before this shows up. I think yours may be a unique situation. At least the service manager acknowledged it and is taking care of it.
BMW car reliability isn't perfect - but in my honest opinion, good enough given the other qualities. I have an X5 in my stable that's had a few bugs, but nothing major that would scare me away. My next 2-wheel and 4-wheel purchases will still be Beemers. If you like the 330, I'd say go for it and enjoy. I've driven one myself and it is an awesome car.