One other possibility is that Font Book's font cache is corrupt or "unhappy" as we sometimes say at work. It won't affect the font from being used by things other than whatever program has the bad cache. We get this a lot with Quark when we have to install new fonts on our older systems.
If you aren't deep into work, you can try
Font Nuke which is a free utility to clear out all your font caches system wide. They get automatically rebuilt upon restart or when you open an application again so there's no serious harm in doing this. However, as with anything that modifies your working environment, I'd recommend you get things done you have to do first while things are still functional before trying any fixes. I've
never had a problem using this utility and have used it quite a bit on multiple systems, but that doesn't mean that something couldn't happen to someone eventually. Don't want to get stuck unable to finish your job because of something you tried to fix.