I have this new problem, my unity theme falls back to some old gnome theme which makes the whole look and feel absolutely horrible.
Here is the screenshot right after login:
And after sometime, theme changes to this:
Any idea how to fix this?
It looks to me that your system is changing your theme to one that uses the Faenza icons set. Check if you have any themes that use these icons on your system and if you don't want it, just remove it. That maybe will do the trick.
By the way, do you have something in