Right, I finally got this to work.
Problem with the process: Cursor remained behind the browser and would not come to the front. Pressed minimize button on browser, and suddenly AS was now on top, with the browser behind it! (Ie the browser did not minimize, it simply went to back. Odd.) But now the cursor could be used to select the portion of the webpage required. Had to do this twice, as the first time the AS Options screen was covering a portion of the area I wished it to capture, so I had to move it out the way, and try again, as it stayed on top even though the "On Top Behavbr □ Keep on top of other windows" box was unticked.
Conclusion: A very useful program, but still has a few quirks to get used to.