It's happening to me too. Only solution I've found, is to delete and re-add one of the tags I can see, when I open my hidden tags. The bug support website is down, and the solution only works on the page I'm on. Hopefully someone know how to contact someone who can fix it.
Lloyd said: If the tags are on the same line then the exclusion is for the conjunction of those tags. Are you putting all your squicks on separate lines?
Hold on, I'm going to go try putting them on different lines.
Does the blacklist work for artists? Mine works for general tags, copyright tags, and character tags. However, I can't seem to get artists blacklisted. Is there something special you have to do?