Xcode creates MainMenu.nib in new project even in version 3.2.5.

Xcode is creating a MainMenu.nib file instead of a MainMenu.xib file when you select File | New Project. Your Xcode version is 3.2.5 (more or less). This should not be happening. It should be creating XIB files so you can check in Interface Builder files into SCM.

Why is it doing this? You probably upgraded from some old version of Xcode from some old version of OS X. I originally started on Tiger (10.4), and have upgraded straight into Snow Leopard (10.6). There is cruft left from the old installation from years back. Delete these files under /Developer/Library/Xcode/Project Templates/Application/Cocoa Application/Cocoa Application. Notice the dates!

UPDATE: Oops! Except for TemplateChooser.plist, which has a date in the year 2010. Don't delete that!

This thread on Apple support discussions is what lead me to this solution.