In answer to my own question above, 'yes, there were battery problems with other operators' and 'yes Boeing did know about it'.
At least 100 batteries failed on 787 fleet | Business & Technology | The Seattle Times
“We have had at least 100, possibly approaching 150, bad batteries so far,” the person said. “It’s common.”
According to that article the majority of the batteries were returned because they had gone so low that a low-voltage cutout was activated.
This sounds more and more like a charging/monitoring problem. Lithium-Ion batteries have a shelf life of two to three years so none of these batteries should have been anywhere near 'low voltage cutout' under normal operating conditions.
It would be interesting to know whether it was a random spread of batteries from 'aft' and 'main' that were returned, or whether the batteries that 'went low' mainly came from one area or the other? That information would help a lot in the diagnosis of this problem as each battery sits in a different electrical system.