That might be of several reasons.
First, verify that you don't have it to explicitly require the rubygem in environment.rb. That is, if you have a line like this:
config.gem "ruby_gems", :version => "1.3.1"
Then you'll have to remove the version from it.
Also, seeing that the rubygems-update gives the incorrect version, you might want to uninstall it.
sudo gem uninstall rubygems-update
Since you have updated it, that gem is not necessary anymore.
I don't think it will help, but I would probably uninstall the macports version of rubygem as well since that might create collisions, even though it doesn't seem like it in this case.
Update:
Since you are using the Ruby from the operating system you don't have to install rubygem through macports at all.
To remove it:
sudo port uninstall rubygems
After that, make sure that you have upgraded the correct rubygem (the binary shows correct, but perhaps there is something missing)
sudo gem update --system
After you've done that. Open up irb (that is, irb and not the rails console) and check the following:
require 'rubygems'
puts Gem::RubyGemsVersion
Also, if you could paste how your apache/nginx configuration looks like, I doubt there is anything wrong in there, but you never know.