When I started with JRiver, tagging seemed like something it didn't do all that well. The interface was just this pane on the side with a big list of tags and it didn't seem to have all of these specialized features that other tagging programs had. So I used an external tagger for doing cleanup and adjusting filenames based on tags.
Then I started messing around with the tag editor in JRiver MC to fix up some compilation albums that showed as multiple albums. Pretty soon, tagging seemed pretty easy with JRiver. All I had to do was select the songs or albums I wanted, using any view I wanted, and then press Tag to work on the tags. It all seems rather obvious now actually. Sometimes I'm a slow learner. A few weeks or so later, I was thinking about the program I had been using to do tags externally and realized I hadn't used it in weeks, despite having adjusted lots of tags to be correct.
Album art was a different story. From the first try, I really liked JRiver's album art maintenance tools. Simple, easy, and they just work.
What I'm saying sort of slowly here is that you probably don't need an external tagging program. JRiver can do *most* of this stuff quickly and easily. I haven't really given Yate a try, but I also don't really have any need for an external tagger any more. The only real reason I would see to use an external tagger at this point would be for songs that have no tags, or completely broken tags. ...and in that case, something like MusicBrainz Picard is going to be the right approach probably. On the other hand, JRiver can *also* fill in tags from file names, so you can use JRiver for that too if that's part of your tagging needs.
For your problem file that won't update, try editing it's tags in JRiver and see what you get.
Good luck!
Brian.