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.
Sorry if my advice was wrong.
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