Yes, this always shows selection horizontally, but it cancels the "center vertically" functionality. I see the same results with:

            editor.setSelection(cursor.from(), cursor.to(), false);
            //cm.scrollIntoView({from: cursor.from(), to: cursor.to()});

I think the problem may be that the Editor.centerOnCursor() function passes null as x position to this.setScroll(). Maybe that used to work and there was a change in CodeMirror. Try looking into cm.scrollIntoView() to see what it's doing.