Hi,
Sorry for "disappearing"; I tried a few projects and workspaces here and was always able to see the same expected behavior as you: i.e., the C/C++ search could not find strings in inactive code.
However, trying File Search with all defaults found them without trouble - all instances (active/inactive).
My workspaces have a mix of copied and linked source files, therefore that does not seem to be the trouble.
One detail that you may try is to re-index your project (or projects). You can select one or multiple projects, then right-click and select Index --> Freshen All Files
For details about the indexer, go to menu Help --> Help Contents and search for Indexer.
Hope this helps,
Rafael