I had a really weird thing happen once. A guy brought me his Strat, and he said the neck pickup all of a sudden got really loud and distorted sounding. It didn't matter how far you lowered the pickup. It was much louder than the other two.
There were Duncan rail pickups. He had installed them himself, and when doing so, melted a wire on the neck pickup, and the wire ended up getting stuck on the magnet and made contact with it. I think it was the white wire.
When I pulled the wire free, the pickup went back to normal!
I've been wiring guitars and making pickups for a long time, and I still have no idea why that happened. For some reason that made the pickup crazy loud. If it happened once, it could happen again.
So maybe check out that lose wire you had, and see if the rest of the wired are OK.