I'm not exactly sure what you mean by 'parent window' and 'move it off the main window'? If you mean Screenshot Captor's window, it is minimized all the time to systray icon, I do not have any dialogs come up related to screencapturing (it just quietly autosaves).
So, I moved my desired active window away from the other programs' windows. I put it out over my desktop, which has no wallpaper or other effects, and is set to black background color (though aero is on which has its effect).
This screenshot has a very small border with the shadow, around the active window, which I assume is the intended result with the default setting.
I tried a few more screenshots, positioning my active window over different windows from various sources. Some have the big border problem, some have the tiny shadow border. So yes, you're right -- there must be some difference in handling depending on what window is behind the active window.