When performing an Active Window capture, SC tries to use an advanced method to capture partial-transparency that can be seen in some Windows themes. This slows down capture, and for some apps could result in strange behavior (for example when the active window is a child window on top of a parent form).
Try this, disable the option "Try to capture Aero Glass transparency effect" on the "Window Capturing 1 tab:

Let me know how that works for you.
ps.
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