Had a similar issue with a Gibson Custom Shop Les Paul.
After four different luthiers in the LA area finally found out that the bridge pickup would vibrate due to the harmonics of certain notes and height adjustment spring/pickup vibrating.
Found it after pulling out the bridge pickup, then listened very closely to the acoustics. We could here something vibrating on certain notes (always Db). Checked internal wires, nada.
Manually held on the bridge pickup and the dead spot/bad notes went away. Checked the pickup, ok.
Found if we put a small piece of silicone tubing, (stolen from a strat) under the pickup adjustment springs, the harmonics would go away and it played fine.
Check to see acoustically if it happens, then focus on if it's a chord or note issue, then pick hard then soft. Try to isolate where the harmonics are coming from. One string, combinations, etc.
I would suspect it could be in the pickup mounting. Often times this is why one guitar sounds awesome and another doesn't. Or a great one goes to a good one with a luthier "tune up".
It's also one of the reasons D. Gilmour likes the single ply pickup covers. More harmonics.
Sometimes, it's just magic..
