I'm not excluding a bum string 100%, but its behavior is indeed the same of a proper dead spot.
That is, changing headstock mass does alter how the note sustains and the note is fretting perfectly. Fretting the octave higher note as well (7th fret, G string) substantially improve the sustain too.
I must say, also, the same thing (even if it is almost unnoticeable) can be said for the open D string. 5th fret harmonic on the D string as well as the 7th fret one on the G string sound a bit strange, too. This neck/body combination doesn't like the D...
EDIT: also you must note that I'm being very picky here. The note is not completely dead, but if you pay attention its sustain is indeed shorter. It took me a month to discover it and now it's more like a psychological thing to me