Multiplexing pins 128/130 RTS/CTS not working

We have wired out both UART2 and UART3 to 9-pin connectors, using UART3 in 3-wire mode and UART2 in 5-wire mode (Apalis names for the UART). UART2 running with hardware flow control enabled and connected to a computer doesnt work, no data is received at either end. By turning off flow control at both ends we can send/receive data perfectly. We have double checked the cables and pinouts with everything matched perfectly with the documentation. We suspect that the pin 128/130 RTS/CTS is not in the right state as they are multiplexed with the SPI function which is the primary operation for the pins.
How do we check the state of the pins that they are setup for RTS/CTS and not SPI?

HI Robert

Welcome to the Toradex Community!!!

Could you provide the version of the hardware and software of your module? Which is version of the Ixora Carrier Board?

Apalis_T30_LinuxImageV2.6_20160701
When i write command “uname -a” i get “Linux apalis-t30 3.1.10-V2.6b2”
Ixora V1.1A

Not sure why or what I did but it seems to be working now. I buzzed out the connector and then played with the GPIO software changing the pins away from UART mode and then back, and it seems to be all fine now. I have rebooted many times and RTS/CTS now seem to be working.

Pefect, that it is working now. Thanks for your feedback.