Some first time mothers fail to care for their litters or don't build proper nests to keep the kits warm. That is not the same as losing weanlings to enteritis.
Are you sure there wasn't a predator roaming around their cages about the time the kits died? It's another possibility. Rabbits can die of fright if something is trying to get to them.
When you said you had the babies out, did you mean you had them out of the cage and on the grass?