When I looked at the Chameleon96 schematics, I noticed a difference in the low speed connector pinout compared to the 96Boards CE spec.
Pin 3 is UART0_CTS in 96Boards, but UART1_RX in Chameleon96 schematics.
Pin 7 is UART0_RxD, but UART1_RTS
Pin 9 is UART0_RTS, but UART1_CTS.
Why have RTS, CTS and RxD switched places?