Could be a performance-related issue ? I haven't fired up X-Plane in ages but AFAIK, although it supports extended resolutions the engine does not "spread" performance equally between the two monitors (or sth to that effect). Weird that you would notice it when looking up/down and not left/right, though.
Apparently there's a clever way of using slave view with multiple instances of the program, dunno if that'd help but it sounds perfect for asymmetric multi-mon:
http://forums.x-plane.org/index.php?/fo ... e-windows/