The bug can be easily reproduced like this.
Press Alt+K to open the color dialog.
Create a new color scheme and name it "Color Scheme"
Create another color scheme and name it "Color Scheme (Alternate)"
Select "Color Scheme (Alternate)" as your color scheme
Close the dialog
"Color Scheme" will be selected as active scheme
I don't know what exectly the problem is, but i think it has something to do with the brackets.
As i wrote in the topic, it IS a minor bug