Yeah, I have a set of night cloths I always use too. Different than regulure hiking cloths.
Anyway, the general concensus seems to be one of:
1) Over washing (mild soap, half or less quantity, only if needed)
2) Possible contamination from comercial washers (detergent.)
On another vein, one thing that was not mentioned was bugs. I have had some pretty nasty bug incursions into my fly tying gear, eating my hackle/wing materiel. If the bag was stored at all damp, this could also be the problem. Spraying with a good insecticide is by far the best for combating those. After a week spray again. After a few days, wash in warm water...in the tub. But, this is permanent damage, too. It happens quite a bit in NY, but we get pretty humid conditions spring, summer(some years) and fall. Anyway, this damage will often result in a lot of loose barbules floating around (like short threads) than easy wind up as little balls after a washing. The bag will also have a disinct "wild" odor from their sheit. You kill all the adults, you kill eggs, and you kill newly hatched ones, soo, timing is pretty critical. I have never had this problem with one of my bags, but it is certainly possible.
(Anyway, assuming you have dried the bag pretty well over the past three or four days.)
To repair the down is probably not feasible. You mentioned it was overfilled by WM. Soo, it should be at least up to factory specs. Spray it with insecticide as outlined, just to be sure about the bugs.
For future use:
1) Use night cloths to keep the bag clean.
2) Wash in a tub, one or twice per year, as needed.
3) Periodically, put it in a dryer with some balls.
4) Keep the down dry, never stored damp, even if it means putting it in the dryer when you get home. (I do that a lot, anyway. It helps a bit with lofting.)
5) Store it loose, as always.
With the overfill installed by WM, you should be happy with the bag. Some experiences with items can leave you with a bad feeling about the manufacturor...look at car owners. I would venture to say you could easily sell the bag here and get a Featherd Friends or similar good bag. Make sure to post about the down damage and the replaced overfill done by WM to be honest with any buyer.
My thoughts only . . .