I use DisplayFusion 6.0.0b5 on Win8.1 with Classic Shell 4.1.0 (http://www.classicshell.net/)
With DF 6.0.0.b5 there is no Icon from file manager Total Commander (http://www.ghisler.com/) in the taskbar on 2th monitor.
No problems with DF 6.0.0.b4
We've just released a new DisplayFusion beta version and this issue should be all fixed up. Please let us know if you run into any trouble after updating.