What was wrong
Nobody had compared the twelve listings side by side. Each one looked fine on its own, but together they didn't match, and the branches missing from the map pack had no way of knowing it. Google doesn't tell you when you're not being shown.
The name, address and phone number were written differently across directories and on the company's own site. Google checks a listing against everything else it can find about the business, so those differences weakened each listing.
Reviews were the other problem. Some branches had a steady trickle, others had nothing recent, and nobody was asking for them. That's common, but it meant the weaker branches kept slipping.