I'm not sure whether this is a bug or whether it is by design.
When you search for something that you have flagged not to see, the questions disappear appear from the results page. I assume this is because they have a tag that I have hidden.
Example, I have MySQL hidden from the main questions and Sql-Server as a favourite tag. Earlier, I searched for a post that had Sql-Server and MySQL in the tags, and the questions were hidden.
In my opinion, if I have searched for something that is in my "hidden" list, the results should appear.
Simple re-pro, search for two tags in the same seach, one in your favourite list the other in your hidden list and see what happens.
Note: Thanks to the first comment, I might have made my self unclear. You need to add a search term in after the tags. Eg: [mysql] [sql-server] connection where mysql is ignored, sql-server is a favourite.
Like I said, this is probably by design, but it could be a bug; it's hard to tell.