Intellij IDEA doesn't grey out some unused methods

Most likely it's not a bug, it's a limitation for performance reasons. Methods likely to take a long time when searching for usages are skipped.

A workaround is to run Unused Declaration inspection explicitly in all your project via Analyze | Inspect Code or Analyze | Run Inspection by Name. That'll take some time. You can also set up TeamCity server to do it for you automatically every night.