right ok, so im assuming you are using the Active Window Capture mode, and its giving you those extra margins that include stuff you don't want.
what you are seeing there is the effect of a CHILD window on top of a parent, combined with SC trying to capture background transparency around the edges.
the quickest best solution is probably to tell SC to stop trying to grab the alpha transparency around window -- which will also result in a faster capture.
go to preferences, than window capturing 1 tab, then uncheck "try to capture aero glass transparency effects"
let me know if that helps.