I'm on Lucid x64 and the way to reproduce this is easy:
1) delete ~/.eclipse
2) start eclipse as a regular user
3) try to install some third party plugin
4) restart when prompted and the plugin is not loaded, although appears as 
installed.

I checked the configuration with the legacy installer and the status for
the custom plugins is "Not included in the runtime".

-- 
Install new software... wont open and I lost all my plugins since upgrade
https://bugs.launchpad.net/bugs/481565
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