Using v0.07 (r635) on OS X Lion v10.7.2
Whenever I minimize (click yellow minus sign) the Cog window to the Dock, you cannot restore the window. Clicking on the Dock icon does nothing. The only way to restore it is to click on Show All Windows and then select the Cog window.
If you hide the Cog window, then clicking Dock icon restores it fine, but if you minimize the window you cannot restore it.