DUE baud rate of 1Mbps.

Have a look for UART_BRGR in the datasheet...
The Due can't achieve an exact 1M baud on any serial ports, the base frequency which has to be divided down is 84M/16 = 5.25MHz, this means 450K Baud is borderline (5.25M / 12 = 437.5K).

You might want to use the native port instead.