There are many times when I switch focus to an application on my Display Fusion secondary taskbar and that application then cannot accept keyboard input. This is especially noticable when I click on a browser and try to open a tab.
I am not sure how to reproduce this error, but it happens around 40% of the time on my system. Alt-Tabbing to the application does not reproduce this issue, only when I click on the item in the secondary task bar.
To resolve this issue I have to focus on another application (or click the desktop) and then click back on the application I am trying to issue a command to with the keyboard.