Sometimes updates to Mail disable the Clip-o-Tron clipping plug-in OmniFocus uses, even if there isn’t a compatibility issue. If you’ve just run an OS X software update that includes a new version of Apple Mail, you’ll likely get an “Incompatible Plug-ins Disabled” error message that mentions that “Mail has disabled the following plug-ins: OmniMailMessageServiceEnabler”.
The good news is that even though the message suggests that our plug-in needs to be updated, it’s already compatible - you just need to reinstall it! To fix this issue, quit Mail, then OmniFocus 2 users should launch the OmniFocus Clip-o-Tron application to install the latest update of that plugin. Follow the instructions on this page to download and install the standalone Clip-o-Tron 3001 installer. We might recommend leaving the OmniFocus Clip-o-Tron in your Applications folder, so that you can quickly locate the installer whenever a Mail update disables our plug-in in the future.
If you’re using OmniFocus 1, open the Clippings tab of OmniFocus > Preferences. Click the button at the bottom of the window to install the v1 Clip-o-Tron 3000, relaunch OmniFocus and Mail, and you should be back in business.