It probably happened for me too - right now for Jabber - when there were too many unseen messages. It showed window and scrollbar was above bottom, and whole window was "freezed", because it was somehow drawing/loading the nicklist (it was empty), after second it filled (at once) the nicks in nicklist and scrollbar jumped at the bottom.
EDIT: For IRC server window same behavior is happening at every time (on this miranda session). And there is also the freeze - right after opening it freezes for few seconds and scrollbar is not ocmpletely at the bottom, then it unfreezes (after 1-2 seconds) and then jumps at the bottom again.
I'd like to know what these freezes are... Or am I the only one with it?