Keith, I have bad news, the bug just came back :S
I was watching a video (to be exact, this one:
http://channel9.msdn.com/Events/windowsazure/learn/Keynote-Getting-Started-with-Windows-Azure) and still had Google Chrome on my center screen, so I separated the tab which was hosting the video and tried to move the other window to my right screen using the DisplayFusion hotkey. Unfortunately the window didn't move, instead it was maximizing again all over my monitors. The hotkey for maximizing the window across all monitors is still unbound!
I'm still using Google Chrome 19.0.1055.1 dev-m and hadn't had any issues since I restarted my computer again due some application setups ( Visual Studio 11 and some SDKs ).
The bug occurs once again in plenty of applications, all running in fullscreen ( windowed/non-maximized applications are not affected ), like Google Chrome, Visual Studio 2010 and 11, Caphyon Advanced Installer, Windows Live Mail and so on... It's kinda annoying when moving windows don't work as expected
Even after restarting DisplayFusion the problem is still presented. For testing purpose I let all applications running over the night until you advice me anything else
The troubleshoot logfile can be found at
http://www.blackcorestudios.de/DF%20debug.txt
[EDiT]
Oh, I should mention that moving Internet Explorer 9, Windows Explorer or some native Windows-Dialogs like the "Save File as"-Dialog are NOT affected by this issue.