Steps to recreate:
1.) Using the Liferay IDE create a new Liferay Plugin project which creates the project in the Liferay Plugins SDK.
2.) Commit the new Plugin project to a Version Control System. (CVS in this case).
3.) Delete the Plugin from the workspace selecting the option to Delete project contents on disk.
4.) Immediately check the project back out of CVS into the now clean workspace.
The project is checked out in the eclipse workspace and loses its association with the Plugins SDK.
This will of course break the Service Builder (and I'm sure other things) because it cannot find the Ant build files that it expects to find in the Plugins SDK.