i may be wrong so if anyone would like to correct me then do so, i think the roots grow upwards chasing the food, from being top fed early.
are you top feeding the cubes? i get the same thing whenever i top feed the cubes for more than past the 10th day of veg. sometimes for my healthy ones, they grow up sooner. when that happens, i just stop the top feeding and start flooding and draining my tables. this stops the roots from growing any higher off the top of the cubes, it has always worked out for me.
the reason why i top feed instead of flood and drain in the first week is because just in case my cubes dont soak up enough water, and the roots arent big enough to reach the bottom to eat. just in case.