I have an E61 and exactly the same issue. My dealer was very coy and tried to charge for the full repair despite the fact we had an extended warranty. We're now in the position where BMW is paying 100% of the parts and 80% of the labour. However, we have to pay for the two hours(!) investigation time to discover the fault.
Having just found these posts, I feel like we're being pretty hard done by, but they have the car and have completed the repair so it's pretty hard for us to argue now...