Yes, this is a bug, but unfortunately a hard one to get rid of. I suggest you use a different approach: In the Builder, use "tagging" to mark the atom(s) that you want colored (Selectrion Tools -> Tags). Select the atom(s) you want colored, add a tag to that selection, run the QuickOptimizer, and then re-select the atoms using the tag. Then you can color the atom(s) from the properties menu.