I searched but cannot find a preference for this nor previous posts in this regard:
I use Desktop Manager (http://wsmanager.sf.net), which may be a source of this problem, first of all. It certainly does create the situation where I'll be on another desktop and if I leave my mouse in the area where the contact list is (on whatever desktop it's on) it will still popup the tooltip-like info box for the contact, even though the contact list is not visible on that desktop.
Anyway, the main problem here is that even if AdiumX is selected (i.e. Adium is shown in the top bar), I can't type in the IM text entry box if the mouse is not sitting on the IM window until I move the mouse over so that it's hovering somewhere within the IM window. Is this a known problem?