"Just for the hell of it, I launched xbmc with "sudo xbmc" instead of "xbmc""
Perhaps by running XBMC as root you're skipping all the settings saved in your ordinary user's home folder (/home/(youruser)/.xbmc). Please report if you can achieve the same result by removing /home/(youruser)/.xbmc folder and running XBMC non-root (but don't forget to back it up; or better just rename it to any other name instead of removing). I'm @work now, so I can't test it by myself.
Now I tried running with sudo xbmc, and I got my sources in my /home/username/.xbmc
so I guess sudo xbmc doesnt skip that dir?