Animations tend to suffer from "flashbacks". If I've understood correctly, this happens when a new animation fails to specify the start or end frames; the old ones can be inherited. At any rate, I do the following, after a special animation (e.g. sitting) is completed. Seems to help, but may not be foolproof.
ActionPlayAnimation(ANIMATION_LOOPING_PAUSE, 1.0, 0.5);
I seem to remember a hak that adjusts bird height (though I can't find it). If all else fails, it's a very easy fix to the model using notepad. On the root node, add a position statement (if it isn't already there), and adjust the z-axis, e.g.
node dummy c_bird
parent NULL
#part-number 0
position 0 0 5.0
endnode
will raise the entire model by 5 metres.
I'd echo Shadooow's caveats.