I have the same problem. This is a bug. Here's how this occurs:

Move an app to a different desktop by right mouse click, move....

Notice the Desk Top manager is no longer always on top.

Right mouse click over desktop manager and notice it says "Always on Top", but it is not.

The painful work around is to reset it by unchecking "Always on Top" and rechecking.

I move my windows to different desktops quite often.

Weird, I have the opposite problem. I want my desktop manager icons to always be on top so I can switch desktops, but on some of the desktops, my applications cover it up.

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thanks for your message.
It is supposed to be always on top. There's no option for disabling that.

Hello, I turn on desktop manager and I think it is good for me but I have one problem, it is always on top, I want it under browser, movie player, ... . Does it possible ?