While it is generally true that nightly builds have far better debugger support and gdb 6 is a lot better than gdb 5, the particular error "Project/Target has no debugging info" is likely not related to either.
You probably enabled "strip executable" by accident (maybe in the system-wide compiler options), so no matter whether or not you have -g in your project, the symbols will be stripped off as the last thing. Reinstalling will have cleared out the settings, so that'll be why it works now.