I only ever updated the one in perl\lib - the CPAN, Encode, and Net directories have configurations for themselves which should be ok. I don't have one in perl\site\lib - so that may need to be kept in sync with the one in perl\lib, if you need to keep it at all (which I doubt).

And please keep the correct capitalisation: it's "Config.pm" not "config.pm" - it's a bad idea to treat these filenames as case insensitive since perl treats the contents case sensitively. It'll just make a mess in one's head to ignore the case. As others have pointed out, "use config" may not end up crashing perl, but it usually won't work as intended either.