Do you use system Perl, or Perl built using perlbrew? What's inside ~/perl5/perlbrew/etc/bashrc? Do you see any differences in root's config files? Search ~/.cpan/CPAN/MyPrefs.pm and the output of o conf CPAN shell command for something unusual in options named make_..._arg and mbuild_..._arg.

It looks like removing these lines made you use system Perl again instead of perlbrew's one, and CPAN is set to install modules in system directories by default.