It's always disabled. I don't have the ability to check/uncheck it.

That's probabaly because you have it set as dockable. It you uncheck dockable, you will be able to check Aways on top.

Along the same lines, I can never get my command window to go to the back. It's always in front.

This is the behavior of the command window when it is set a docakable. Right click on the title bar of the command window and make it un-dockable.