Eh ? Not sure what you mean.. MC does not control how Windows handles the TaskBar.
But MC Control how the MC-Tabs working for Drag and Drop.
Beware Off Topic: My Taskbar is always invisible and when i go with the mouse to the place where my taskbar is, the taskbar stay in the background. Only Win+T or closing all windows make the taskbar visible. (This configuration is only possible with 7+ taskbar tweaker) This help me to use the full screen without being disturbed from a taskbar-popup. But this is off topic, sorry. /off topic
My Tabs in MC are on the bottom and my taskbar is on top of the screen, therefore i have no such Problems like jean.