Open Xcode->Preferences->General and make sure "Open counterparts in same editor" is unchecked. Then open your project and close any files which are currently open by selecting File->Close File "Filename.h", etc. from the top menu. Make sure to close any files which are open in the project window's editor panel as well as any files open in separate windows. Only the project window should now be open, and its editor panel should be empty.
Next double click on any source file (e.g. mySource.h) to open it in a separate editor window. Don't open any other files. Your only Xcode windows should be the project window and the single editor window just opened.
Now click on the Grouped/Ungrouped icon (second from the right end of the top toolbar) in the editor window so that the icon is set to Ungrouped. Next close the editor window by selecting File->Close File "MySource.h" from the top menu, and then close the project window as well by selecting File->Close from the menu.
On reopening the project, each editor window you open should now be set to Ungrouped. However, for other projects, you may need to repeat the above steps in order to clear the Grouped setting. The editor windows for any New Project should be set to Ungrouped when they open.
If any editor windows continue to open as Grouped in the projects you've cleaned or in new projects, delete ~/Library/Preferences/com.apple.xcode.plist. If that doesn't help, search all drives which are visible to Xcode for xcode.plist files and delete them. Be especially sure to search the root directory of your boot drive.
Hope that helps!
\- Ray
