Ever since the last one or two rawhide updates firefox does not use plugins in /usr/lib/mozilla. The about:plugins shows only the default plugin. Yet when using mozilla the plugins are there. I have flash and java installed in /usr/lib/mozilla.
I suspect this problem was the result of launching firefox from the /usr/lib/firefox-*/firefox rather than /usr/bin/firefox, which screwed up the environment variables needed to find the plugins in /usr/lib/mozilla. If you upgraded from a test release of FC3, then your gconf keys may still be screwed up. In any case this is no longer an issue with FC3 created profiles.