I've just had exactly this problem, I've just started playing the game through again (3rd time, first time since installing the patch (UK version)) and got exactly the problem described.
Picking another option (not "Alright.. we mean no harm" ), things work ok - I get warned by the handmaiden and Kreia says we should do as they say, I then get the atton/kreai cutscene (in the force cages). Seems like a bug to me, though I don't remember it before patching the game, and I'm sure I picked "Alright.. we mean no harm" the first two times I played the game through.