The problem was tricky to narrow down because if I cycle back and forth between having and not having the ^M characters, reproduction becomes unpredictable.  I think some undesired states were persisting between sessions.  When I started deleting semanticdb files between each run, reproduction behaved a bit better.  I've found that the problematic lines are the header guard:

  // Problematic:
  #ifndef MANAGER_H^M
  #define MANAGER_H^M
  // ...
  #endif // ^M here doesn't affect Semantic behavior

> Could you check if it is parsing the ^M file correctly?  Just do:
> M-x bovinate RET
> and see if it has stuff in it that matches your expectation.

With the ^M after the header guards, I get only nil when I bovinate.  When I remove them, I get more content.