I have accidently stumbled upon the fact that Boxee on Windows indeed runs in a borderless maximised window, and not a true full screen. This implmentation is no doubt due to multi monitor use flexibility. For HTPC - it has limited relevance.
Try it out, press windows key and watch the taskbar appear infront of boxee. Or use the magnifier tool and watch it follow your boxee mouse cursor.
This is fine for high end system, but has a gui performance penalty for systems like the Acer Revo. The gui on Windows is half as smooth as it is on Ubuntu thanks to this fake fullscreen implementation. This is also true for XBMC, fortunately in XBMC you have the option to utilise true full screen in the settings magically giving it a shot of silky smoothness in the gui.
Now not everybody sees the difference with 30fps vs 60fps, yada yada - lets not get into this debate, I can see the difference as night and day. The simple question stands as - is there any way to switch to true full screen in boxee?