As far as actionscript is concerned, the registration point cannot be modified by using ctrl-i or the free transform tool. I admit that flash is rather confusing in that aspect on first glance, but you'll get used to it.
To truly modify the registration point you'll need to go into your MC and move the elements inside relative to the 0,0 point (which is it's registration). If you have a lot of animation inside the movieclip use the 'Modify Multiple Frames' (think that's what it's called...you'll find it), extend the range to cover the whole timeline, and select everything and move it like that ^_^
G'luck
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