If you're online with your studio machine, the automatic software updates should show you whether your version of Pro Application support is up to date. In case it's not, you may want to update. You find it in the Apple menu.
As another idea: You may want to download Onyx from here (it's free):
http://www.titanium.free.fr/pgs/english.html
Run all of the maintainance scripts (read what the descriptons say before doing so, but usually the standard settings are fine, unless you have lots of stuff in your Finder sidebar, which, by default, will be removed). Might take quite a while but it's really an excellent application.
After (or even before) that you may want to manually remove the Kontakt component. It's in library/audio/plugins/components. Also, just to make sure, remove the Kontakt standalone, which should be somewhere in your applications folder
And you may as well want to remove the Kontakt 3 plist file, you'll find it under library/preferences, it's called "com.native-instruments.Kontakt3.plist".
Then you may want to re-install Kontakt (no need to reinstall the library, you can keep it where it is and re-assign the path after the installation) and re-authorize it. Try to start Kontakt in standalone mode to make sure authorization worked. Then install the latest Kontakt update (as said, you may even want to go for the 3.5 public beta, which should be available when you log into your Native Instruments account).
When done with all that, start Logic and see what happens.
There are certain quirks with Kontakt and Logic, but it not passing AU validation at all has most likely to do with the plist file being sort of wrecked up, perhaps due to whatever initial crash that you apparently have experienced.
Fwiw, it's always a good idea to open all NI programs in standalone mode first, before you load the plugin version for the first time.
After all, this sounds like quite some work, but what'll take the most time is Onyx cleaning up your system - might as well be an hour or so, just make sure you've got no computer work to do in that time.
- Sascha