Ubuntu – How does Unity decide the icon background colours

You want to remove the 1px white border around the launcher, right? If that's the case, I believe it's hard coded and it's not something that can be achieved without messing up with unity source code, or in your case - with the unity-rotated one :)

This seemed to be an issue with scaling and Unity desktop.

After I reset the "Text scaling factor" to 1,00 in Unity Tweak Tool and also reset the "Scale for menu and title bars" to 1, the boxes re-appeared without even requiring a logout. Now I am able to resize them again to the 0,875 as is my preference. I do hope that this topic here helps someone who might experience the same behaviour from Unity desktop. =)>