Have you run DiskWarrior? If it reports directory errors, then the logical thing to do is fix them. The only directory errors that AppleJack will fix are the same ones that Disk Utility fixes.
AppleJack can mess up preference files, in that it will put any it *thinks* are corrupt in a special folder and it the application developer didn't use one of two formats for the permissions, AJ will think they're corrupt. So, running the Auto version may not be the way to go.
There are some permissions errors that always show up and are harmless. There's an Apple KB article about that if you look (I'm too tired right now...)