KurtE:
The problem I am running into is I don't believe the USARTs on the Due can run the Dynamixels at their full buss speed of 1000000.
That is, if I understand the baud rates on the Due, when I ask for a baud rate of 1000000, the actually generated baud rate is: 84000000/(n*16). Best fit n=5, so actual baud rate is: 1050000 so off by about 5%, which is not close enough. I believe the spec for the servos is it can handle a delta of up to 3%
Are the servos sending data back to the Due?
If the answer is no, you can try to set the USART in synchronous mode, where the baudrate is generated directly from the master clock, and you can use a divider of 84.
(in the SAM3X datasheet is chapter 36.7.1.3)