Currently dev-ruby/rubygems installs its files into /usr when running with root permissions. It should install into /usr/local by default instead to keep a clear separation between gentoo-managed files and user-managed files. The current situation may lead to problems, especially when users mix ebuild and gem-based installs for the same package. Note that rubygems still needs to be able to install into /usr to support the legacy gems.eclass, and that the relevant /usr/local paths should be added to the RUBYPATH automatically so that this change is transparent to users. One potential issue is that gems already installed into /usr may no longer be removed without providing additional options.
Fixed in 1.3.7-r2.