After a year or so of being affected by this bug, I discovered
a message that appears while doing "apt-get upgrade" for a new
kernel. The message says that LVM was found to not be installed
or running, and the Grub install/update process is switching to
raw device mode. It may well be that the switch to raw device
mode is what is causing it to overlook /dev/md12*.

I'm currently running a freshly-installed Chimaera and using
LVM, and have not seen this bug manifest on that installation.