Mikkel,
Not sure if you're on the developers email list, but Facebook just made a new blog post about iOS6 integration. The link is below, but one specific quote is applicable to your question:
It includes significant new features and enhancements that make it easier to add Facebook to your iOS apps, along with support for the Facebook integration in iOS 6
developers.facebook.com/blog/post/2012/06/18/ios-and-facebook/
So, for now, it sounds like their iOS6 integration may not be fully there. While we don't use the iOS SDK in JFBConnect, I believe there's some work to be done on their end for the Javascript library (which we heavily rely on).
We still do plan to test, but wanted to let you know about that since we just heard about it!
Thanks,
Alex