My E93 used to leak water into the boot area - the dealer had it quite a few times for this issue. In the left side of the boot was a plastic compartment, this used to always have an inch or two of water in it during periods of bad weather. There had been modified roof seals prduced that the dealer fitted but it never cured it. In the end the car went back to the lease company so someone else will have had the issues this winter
Hope you get it sorted and make sure you trust the dealer. My local dealer was pretty crap and introduced all sorts of rattles into the roof every time they messed with it
