Perl has 3 paths it checks for modules, site, vendor, & perl. Vendor supplied modules should go in perl or vendor, because the default is site which is where modules you install should go.

You can run this to get the 3 paths printed out in the order above perl -e 'use Data::Dumper; print Dumper(@INC);'

If the core modules are going in to site then the package being supplied by IBM has an install bug and they should fix it. If they are installing in to the right places but modules you install are going to vendor or perl, then you need to force them to install to site. See: http://perldoc.perl.org/ExtUtils/MakeMaker.html#INSTALLDIRS