Whenever I'm logged in and try to go on the homepage, it shows access denied. (This is for the new FM Scout layout) But when I'm logged out, it works just fine.
There was a small time margin like 2-3 minutes that nothing should work properly until the transition was complete. Does it still happen?
I'm dead tired at the moment, as I've been struggling over this upgrade since yesterday evening without any sleep. So it's pretty much possible I might have missed something that could be causing this.
Tomorrow I'll have everything checked all over again to make sure there are no major issues, like the one you mentioned.