Notify-osd notifications appear unthemed in top-left corner

i3 is using "dunst" notification daemon, so you have to remove it in order to re-enable ubuntu notify-osd.

Execute following from terminal:

sudo apt-get purge dunst
killall dunst
notify-send "Hello"

I had the same problem because of i3. Purging all packages that were installed with i3 helped me:

sudo apt-get purge i3 i3-wm i3lock suckless-tools i3status dunst

I think (but I'm not sure) that the problem was with dunst package - according to it's description it is notification daemon too.