Hmmm, the first one is for brightness, touchpad, volume, media control indicators, and is hardcoded, so it doesn't change according to the theme. The second one is from Notify OSD of Ubuntu, and seems to conflict with Cinnamon's notifications. You should remove the package "notify-osd" using Synaptic Package Manager. After removing it, the notifications will be themed correctly according to the theme. The first one will still remain, but don't worry about it - that's by design
