(to aid search)
Often in set ups that use version control the project.pbxproj can be merged in such a way that two CODE_SIGN_IDENTITY lines can be inserted. This seems to cause Xcode problems under certain situations (like command-line builds or archiving).
A tell-tail sign is lines similar to this in the project.pbxproj file (right-click on the project and select "Show Package Contents…")
"CODE_SIGN_IDENTITY[sdk=iphoneos*]" = "iPhone Developer";
CODE_SIGN_IDENTITY = "iPhone Distribution";
Deleting one of these lines will let you select the correct value in Build Settings and the project should once again build correctly.
I have created simple script to help diagnose this issue it can be found here: https://github.com/rjstelling/Xcode-Project-Validate