Are you sure that the perl you are using to run the CPAN shell is the same perl you are checking @INC with?

I would expect the CPAN module to install modules based on the paths specified when perl was built, which suggests to me that you may have two separate builds of perl, one at /usr/bin/perl and another at /usr/local/bin/perl. I'm guessing that your @INC problems involve a script that starts with #!/usr/local/bin/perl.

Use `which perl` to see what perl you're running from the command line, and compare the values for @INC from perl -V:

/usr/bin/perl -V
/usr/local/bin/perl -V
[download]

If they show different paths, you'll probably want to pick one of the perl installions, replace the other binary with a link, and remove the set of libraries which is no longer needed. (To go along with the options in perl's Configure script, I'd suggest keeping /usr/local/bin/perl and making /usr/bin/perl a link.)