If you try to install dev-perl/libnet (home of Net::FTP, Net::SMTP, etc.) it installs to /usr/lib/site_perl instead of /usr/lib/perl5/, /usr/lib/perl5/site_perl, or any other location that perl would expect it to be.
David, I need for you to confirm a few things for me to debug why this is occurrying for you. First, when was your last emerge rsync? I'm going to assume recently, but just to be safe. Second, which version of MakeMaker shows up when you type emerge search ExtUtils-MakeMaker . If this is version -r1, I would recommend re-emerging MakeMaker and then trying to emerge libnet again. I have tested on both of my perl installations (5.6.1 and 5.8.0) and libnet is correctly installing. The symptoms you described were fixed in an update to the eclass for perl modules recently. Thanks! Michael
Bug 9067 fixes this *** This bug has been marked as a duplicate of 9067 ***