I don't know. In our current Project, we scroll scenes when the actor is at a certain point ( e.g. actor can walk around without the scene scrolling, only if he gets too far to the right for example, the screen scrolls ). It's in 1280x800 and the scrolling is the same in fullscreen and in windowed mode. We did not change any of the scrollspeed parameters. So I don't know what the problem is in your case.
(Just for info: On my graphics card the windowed version runs with ~1500 FPS, in fullscreen it's vsynced ( 60 FPS ) )
Greets,
Spellbreaker