This happened to me once on a wiring mod. Try as I might I just could not figure out why the neck pickup sounded so dead until it finally occured to me to test the resistance of the pickup. One of the coils had died.
This happens from time to time, in my case somewhere non-visible.
Now I test the resistance of the pickups before adding them to the wiring harness. Also test the pots, caps, switches, jacks and resistors (if you have them) to make sure they all work right before they go in.
On a different topic, I am thinking Simon should start a thread on 'tips and techniques not widely known.". The knot in the bridge wire, the washer trick, the many uses of veneer... I am sure I can think of more that I have either used already, or plan to in the near future....