Might be the launch configuration that's out-of-step with your build projects.
Open up the launch config (Run-Run...) and then go to the plugins tab to see if the plugins are there. You could click on the 'add required plugins' and it will add them in again.
Or, alternatively, delete all the runtime configurations from the Run tab (at least, the Eclipse and Runtime workbenchy type ones) and then do Run As...Eclipse Workbench, and it'll create a new one with the right requirements.