Sunroof Leaks and Keyless Entry

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Make sure you are waiting for the BCM to react to the remote, before pushing more buttons as said in the bulletin. If you are, then have the dealer test it. I will say from experience, you have to be close if approaching the vehicle from the driver's side of the vehicle or from the rear. From the front or passenger side, the remote has a greater range. This is due to the BCM, which receives the signals, being in the front right passenger area.
Have you tried both remotes? If so, does this happen with both, or just one remote? Does it happen only in certain areas? (Some areas with a lot of RFI can affect a remote. Per FCC regs, a remote on a vehicle is as low as you can go on the interference. In other words, the remote has to give away to any other type of radio frequencies in the area. It cannot interfere with another frequency generator of any type.
For the leak, I suggest a dealer before taking anything apart. If the leak caused any damage to the headliner or any other interior parts, it will be covered under warranty, as well as the repair of the leak itself. When the vehicle is in for the sunroof, have the dealer test out the remote.
You should not have to put up with a non-working remote.