I've got Kubuntu running my HTPC and XBMC starting up in full screen on boot. Besides XBMC's remotes which I operate from an Android tablet, I also use a VNC client on said tablet to connect to the HTPC to operate other programs. As a VNC server, I've got krfb also starting up on boot which is where my problem lies. krfb does not start minimised in the system tray. There is also no option to get it to do so in its configuration screen.
Here is a guide on how I have krfb configured to start it minimised.