how are you running your multiple monitors?

if they're in contiguous mode (monitor A and B) FSX will try to display through all of them

if you have them on 1 and 2 mode (2 separate desktops), FSX will pick the primary screen to work on (your primary screen being, of course, the large one   )

this is set through the video card's options, in the multi screen management tab ( i can't remember the exact procedure without actually going through it, but it should be pretty straightforward)

the main difference between these modes is how windows and applications treat the multi monitor setup... you can still move the mouse across them, and you can still move windows in and out... the difference is that when you maximize something on 1+2 mode, instead of maximizing across all displays, it'll pick a display as it's 'parent'

so when FS goes full screen, it won't try to force the small screen into a resolution it can't handle, leaving it free for undocked panels

hope this helps

Cheers