Seems like the problem is when you have an old project with some subprojects under source control while the main one is not.
I have removed from Xcode Preferences source control completely, and it seems did the trick – now archiving works.
To remove your project from Source Control press command+, (or select Preferences from main menu) -> Source Control and uncheck all parameters.
I am following this issue in the developer forums and seems like Apple is aware of the issues.
New projects are not affected.
EDIT FOR NEW VERSION OF XCODE (6.3.1)
After installing new version of Xcode yesterday I have enabled Source Control and it works now correctly. Below is my version now:
