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

Question

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.

Answer 1

Try the following:
1 - delete the iPhoto preference file, com.apple.iPhoto.plist, that resides in your
     User/Home/Library/ Preferences folder. You may have to use your Admin password in order to move it.
2 - delete iPhoto's cache file, Cache.db, that is located in your
User/Home/Library/Caches/com.apple.iPhoto folder (Snow Leopard and Earlier).
or with Mt. Lion from the User/Library/Containers/com.apple.iPhoto/
Data/Library/Caches/com.apple.iPhoto folder
3 - launch iPhoto and try again.
NOTE 1: If you're moved your library from its default location in your Home/Pictures folder you will have to point iPhoto to its new location when you next open iPhoto by holding down the Option key when launching iPhoto.  You'll also have to reset the iPhoto's various preferences.
NOTE 2:  In Lion and Mountain Lion the Library folder is now invisible. To make it permanently visible enter the following in the Terminal application window: chflags nohidden ~/Library and hit the Enter button - 10.7: Un-hide the User Library folder.
OT