I did look at this with some more details.
I think your problem is that you use own_window_type desktop. This just sets
the _NET_WM_WINDOW_TYPE_DESKTOP atom, which apparently metacity and beryl
handle by stealing the focus if you click on the desktop.
Beside this, conky only uses this to decide if mouse press buttons events on
the conky window can be propagated.
Therefore, I don't see this as a bug in conky, more as a window manager
"feature".
You can simply solve it by using a window type of normal or perhaps override.
** Changed in: conky (Ubuntu)
Status: Incomplete => Invalid
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Conky hides itself behind nautilus desktop
https://bugs.launchpad.net/bugs/537499
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