Thanks Miroslav,
Unfortunately the SDK kernel we have is not booting on our custom hardware, and I have not looked into why yet. We have downloaded/configured/built the kernel (3.12) as follows:
http://wiki.beyondlogic.org/index.php/BeagleBoneBlack_Building_Kernel#Compiling_the_BeagleBone_Black_Kernel_2
Yes OMAP_MUX is set to 'y'.
Is this feature something specific to SDK kernels? If so I can look into getting the SDK kernel to boot on our board.
Thank you - Anthony