Thanks, adding ~ and /usr/local to the Search Scope did the trick, although I was thinking that the Search Scope was just for Default Results (i.e. those without a command/keyword prefix), not file-specific (open blah blah) results. Guess I have a bit of retraining to do.
Also, in the FAQ, there is an article that references these sorts of problems (http://support.alfredapp.com/kb:indexing), however it also references a scope-like setting under the File Search tab that I can't seem to find.
Again, thanks for your help.