In the Transformers: Prime two part episode "Operation: Bumblebee", It is revealed that the reason his voice box is permanently damaged is due to being captured, interrogated, beaten severely and left for dead by Megatron himself. Ratchet, The Chief Medical Officer of The Autobots, was able to save his live and able to make him nearly whole again, with the exception of his voice box. Shortly after, The Main Characters of this series ended up on earth where Ratchet simply doesn't have the proper technology to finish fixing him.