This in general looks like a hard reset configuration issue. Parallel Ethernet ports share pins with USB, SGMIIs can potentially conflict with PCIe.
Therefore, technical support's suggestion is to ensure that RCW does select the interfaces you wish to utilize and that you don't attempt to use port combinations that are mutually exclusive.
Details can be found in P4080RM, sections 3.5 and 4.6.4.
Also, please be informed that Silicon Image 3124 is not a Freescale product, we did not test any driver for it with any version of the SDK. If there are issues with the driver for that peripheral, our suggestion is to contact the driver maintainer or the chip manufacturer.
I know that you has an open Service Request for a potential issue for their device tree. Checking a device tree source code is a time-consuming procedure, you're suggested to wait for response to SR 1-1083755035.