With the Alder wood body being a natural wood (compared to the DBK I also use which has the 'processed manufactured' wood) there could have been inconsistancies in the wood opposing certain harmonic frequencies. As for the electronics, they were fine. As for the neck, it was one of the best necks I've played. I checked the wiring and the outputs, they were spot on.
The quick demo I gave to the rep to demonstrate the issue was - I got a 'light crunchy' sound (not a lead sound), and did a 6th fret harmonic on the G-string, pulled up on the bar, down on the bar and back up .... the note dies! With the 2000 DBK, and now my 2002 VBL (with Lo-Pro), I can strike the harmonic with the same light crunch sound, go up and down on the bar at least 5 times before the note dies off.
It would be good if you can try it.