Not sure if there is a lot I can add to this, but I'm experiencing the same issue. No matter what I do I can't get the clip-o-tron to cut my messages in the new mail 5.0.
- Used a variety of keyboard shortcuts (cmd-opt-ctl-c, cmd-shift-opt-c, ...)
- Reinstalled and removed the plugin
- Restarted computer
Totally rely on this feature and am sad to see it not working.