The BIRD is responsible for connecting both batteries so they charge when either one is being charged. There is a time delay before that happens but it's only a couple of minutes.
I had a similar problem. Sometimes it would charge, sometimes it wouldn't. In my case it appeared that the BIRD only worked part of the time. Perhaps a bad connection on the circuit board or a defective component in the circuitry.
I replaced the BIRD (a fairly cheap DIY procedure) and all my problems went away.