I have a test application using the Lync 2010 SDK in full UI suppressed mode. When the video is started by either party, on some computers the VideoWindow won't display in the panel that I provide the handle for. It instead is displayed on the upper left hand corner of the screen. This also happens with the sample applications provided (I am also using the example code to display the VideoWindow on a panel).
I did notice on machines running windows XP the video consistently is display in the proper location. Only on my Windows 7 test machines do I have an issue with the video location. If I don't mess with the window style and allow the border, the window title says "ActiveMovie Window".
The only thing I can think of is that it's somehow related to the Windows User Account Control (UAC). I've seen issues in the past where Lync/Communicator runs under a different UAC level than the app.
You could try disabling UAC on the machines that it consistently fails on, and see if that makes any difference.
Edit: The theory here is that it's the SetParent call that's failing. I can't remember off the top of my head, but is there a return value from SetParent that you can check?