If I display two buffers side-by-side and scrolled the window up and
 down using the scrolling wheel of a mouse, most of the time only the
 right hand side window will take effect even I select the left hand
 side window by putting the cursor at the left side window. Sometimes
 the problem disappear if I quit the editor and started it again,
 however, this solution didn't always work. 
I have some code I wrote to handle the scroll wheel. It scrolls the
window that the mouse is in, but does not select the window. You can
find it at 
http://xemacs.seanm.ca/ under intellimouse.
Cheers,
  Sean MacLennan