I think 6 weeks is a long time to leave her in with her offspring. Her boys are fertile at 5 weeks.

They are really ready to go at 3 1/2 to 4 weeks. I also give my mothers a very long break. 4 weeks recoup time in a social setting with only females.

Besides that, how are they (pups or weanlings) killed? Rat mothers kill in two different ways. One is where they dispose of weak or dead individuals by just eating and nibbling on them. As if they were eating food or a snack.

The other method is a bite to the spine/ neck with intention of actually culling them. Most often seen being used in older pups.

Have you examined the bodies to see how they were killed? It's common for animals to eat the best parts to get extra nutrition. Not surprised that she would have eaten the brains and stomachs.

See If it was her doing or they died themselves? Another idea could be something pathological in your colony.

If I were you, I would do some investigating into this problem. If it were just aggressive mothers, I would dispose of them. But since this seems to be such a widespread problem makes me think there is something else going on with this colony.