There's a discussion of this issue on Apple's paid developer forums. It's a bug in Xcode 4.5. Apple's engineers are looking into the issue, but there's no fix yet.
There are two workarounds. The first workaround is to run your command-line app from the Terminal. In the Xcode project navigator select your executable from the Products folder. Right-click and choose Show in Finder. Double-click the executable in the Finder to launch it in the Terminal.
The second workaround is to install Xcode 4.4. Choose Xcode > Open Developer Tool > More Developer Tools to access Apple's developer downloads site.