I have changed the full-screen application detection code in Beta 20 and released a small update. Just extract the attached DisplayFusion.exe file to your DisplayFusion installation folder. It will still have v2.2.120, but the .exe file's timestamp should be "Feb 16, 2009 11:59pm".
Edit: Update removed - please download Beta 21 instead.
I just now ( literally) got the update via the auto update -do I still need to apply this patch?
I am I.
You will need to apply this update. I am re-packaging Beta 20, but if you just got it then you will have missed this update. If your installed version of "DisplayFusion.exe" has a timestamp of "Feb 16, 2009 11:59pm" then you are running the latest version.
Update: I have just re-released Beta 20 with this fix included. If you download the installer anytime after this post was updated then you are all ready running the latest version.