I also had firefox 2 working fine with aMule, but since I changed to F9, and Firefox 3, association stopped working. Not it complains that ed2k protocol is not associated to any app, but the entries are there in about:config, so I'm lost.
Regards.
Edit: I found the solution, I had to create this boolean preference in about:config
network.protocol-handler.expose.ed2k
and set it to false. After that, I clicked over an ed2k link, and firefox asked me which app I wanted to use to open the link. I choose /usr/local/bin/ed2k and it worked!
Regards.