Version: 1.6.12, Build 2416
Not sure if there is a setting I am missing or it's a possible bug?
If I move the DM (desktop manager) into the taskbar and change desktops the DM seems to end up under the taskbar on the switched desktop. I will provide two screen shots.
As expected here

The taskbar overlays DM. Unable to click at this point

Recreate:
If the DM shows after switching desktops hover over an application icon in the taskbar. Shortly after the task bar will cover the DM
( Fantastic Application! )
