maybe this bug is already reported but I did not find it.
Since win7 I have the issue that my titelbar button gets "binking" in the foreground but it's corresponding window don't have focus!
I think you can see it very well in the attached picture.
My spec:
Win7 Enterprise x64
DisplayFusion version v3.3.0
Could you try the latest beta version of DisplayFusion 3.3.1? We've made quite a few improvements to the TitleBar buttons. You can download it from here: http://www.displayfusion.com/Download/Beta/
Does this seem to happen only when you come out of standby or hibernate, or if the monitor configuration changes (i.e. you disconnect or add a monitor)?
I actually reproduced this issue by accident yesterday when I disconnected my monitor from my laptop, but haven't been able to get it to happen again.