Random question: Is she scared or intimidated by the skill at all? Sometimes even the kids excited to get a bh, and have it with a spot, land on their knees at first. People tend to tuck when they're nervous doing a skill, which results in landing on their knees for a bh.
Another possibility is what I like to jokingly call the 'omg I'm alive!' response. When first getting a bh on their own, some kids leave their hands and feet in contact with the floor rather than blocking and landing only on their feet. It's a safety thing again. With all limbs in contact with the ground the risk of falling is gone. I usually see this the first few atempts by a gymnast to do a bh without a spot, it's something they stop doing once their comfort level with the skill goes up.
BH is the skill that has the widest range of responses once a gymnast is ready to do it on their own I find. Some take right to it, some maintain a perfect one with a finger 'spot' yet fall apart when doing it on their own. It's a pretty pivotal skill, a gateway to more intermediate/advanced tumbling so there is a lot of hype attached to it.
I kept my response limited to the mental possibilities because without seeing her do it, it's too hard to speculate. Have you asked her coach at all what's up? My other question is, is she blocking to her knees, or are her hands still on the ground when she lands on them?