Ran into this the other day, with a solution presenting itself on launchpad as usual. This is more of a workaround than a bugfix, but it works perfectly satisfactorily.
Essentially you want to change your Blender launch parameters to something along the lines of:
blender -w -p 0 0 800 600What this does is tell Blender to launch in windowed mode, as well as starting at the bottom left of your screen and at a resolution of 800 by 600. You can then move the window around and resize/fullscreen it as per the norm. For some reason Blender throws a hissy fit and refuses to start windowed when only the "-w" parameter is specified, the additional options seem to force it to work properly.
Assuming you're using Gnome, you can customise your menu entries by going to System > Preferences > Main Menu.
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