I haven't found any application other than some of the Microsoft Office 2007 programs that are affected by this yet, but the problem is quite severe.
If you open to Excel documents, and place them both on the secondary monitor, the DisplayFusion taskbar displays both of them as "active." This means that if you have one of the excel windows active, you CANNOT switch to the other excel window. Clicking on the other Excel window's taskbar item just minimizes/maximizes the currently active window. I am sure this is due to the way these programs manage their open windows, but this problem does not exist in UltraMon, so surely there must be some way around it.
Steps to reproduce:
1.) Open two (or more) Microsoft Excel documents, place both of them on the secondary monitor (the one showing the DisplayFusion taskbar).
2.) Focus on one of the Excel documents (i.e. make it the active window).
3.) Notice both Excel documents appear to be "active" in the taskbar, but only one document is actually in focus/active.
4.) Try to switch to the other Excel document by clicking on it's taskbar "button."
Glad to see you got this handled. Do you have an ETA on 3.0.4?