Thunderbolt and Superdive PCIe ports don't work after logicboard replacement.

I recently had my 2011 MBP motherboard replaced by Apple because of the common GPU failure. I got it back with these issues:

• The DisplayPort portion of the thunderbolt port still works, but the port will not even power a thunderbolt drive.
• I have an HDD in the Superdrive slot, and it is also not recognized.
• I replaced the HDD with the Superdrive and it works, but an HDD wont.

I'm guessing that this is some sort of controller issue, potentially involving a plist issue.

Any help?

Thanks.