1. Create any Java Project.
2. Enable CDI there.
3. Build the project.
4. Delete the project.
5. Create a new project with the same name.
6. Enable CDI.
7. Build/clean-up/re-build the project. CDI validator won't validate the project until Eclipse is not restarted.

The reason of this issue is that WST doesn't initialize validation helpers if a new project with the old name is created.