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
Re-open it
"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
