Mouser, thanks for taking a look at this.
The only app that doesn't work properly with SCC is Firefox, starting with version 4, and now with version 5 too. I can capture the whole desktop and get whatever's showing in Firefox. If I try to capture FF as the active window, I get just the window borders, no contents. Pretty much what the attachments in my first post are demonstrating.
Capture Object mode in SCC with the red box was working as expected until Firefox 4 came out -- I could get the tabs, menu bars, sidebars, and the contents of a tab; that stopped working with Firefox 4, I could only get the entire application window, and for FF5, only a blank window with borders. The red box will only come up for the whole app window, not for any objects within as it used to do for FF 3.
I can capture whatever I want in any other app with SCC, it's just the two most recent versions of Firefox that are misbehaving.
If I exit SCC and do alt-prtscr, the 'active window' capture works fine for FF.
Yes, if I capture the entire desktop, SCC auto-selects the region of the active window.
I did look at the accelerated graphics setting, and it appears to be turned off.
I'm writing docs for a web app, and the current situation isn't a showstopper, just a couple extra steps for cropping & fiddling to get to where I need to be. Everything else about SCC is awesome; the users just love the drop shadow effect :-)