I believe that since the clip is not included with the tool (i.e. sold separately), it isn't covered by the warranty. Now if you broke the clip on one of their newer folding knives, I believe that would be fixed/replaced.
Also, I would try sending the broken clip and a letter through snail mail. You might get a better result if they have the clip in hand and can see it's broken. I find that e-mails don't always get the best result.
Finally, I forget if Leatherman has a warranty card or not, but I know that some companies won't help you at all if you haven't previously filled out the warranty card and sent it in.
Hopefully that helps. In my experience Leatherman is normally a pretty stand up company. When I became an Eagle scout Tim Leatherman sent me a letter of congratulations and a Wave multi-tool.