Hi Shawn,
Please let me know the exact program and the edition of the current Windows 7 system.
I tested in using Windows Live Messenger. I opened some windows and let them combine to one icon. When I receive a new message, the icon will start flash. When I put the cursor to the icon, Aero Peek will occur and the activated window are also flash in the list. I attached a screenshot of the Aero Peek.
If it will not work on your computer, let's create a new account to see the result.

If there is any misunderstanding please just let me know. If a screenshot can be provided it will be much appreciated (please just upload it to skydrive.live.com)