Verify that "Look in:" on the References tool window is set to what you want, likely <Current Workspace>.
Also, verify that "Show all" is checked on the References tool window.
You can also try rebuilding your workspace tag file (Project > Retag Workspace...).
Otherwise, you should *at a minimum* see the reference in the current file which you originated the reference search from, if that is not happening, you should post the source file, perhaps there is a context tagging issue specific to that file or the specific language.
References can also be broken if you change the identifier characters in your language-specific color coding settings in an incorrect manner, so if you have modified color coding, you might want to double-check that also.