Well, if the BCR isn't charging, I suspect the charging circuit of the 5V board may have a problem. It'll run for some time on a new battery until it discharges that battery.
If you want to see if the charge circuit is working, get things all hooked up and connect a voltmeter to the battery leads while it's still connected to the locomotive electronics. Apply track power. If the voltage doesn't start moving up when you do this, it's not charging.