The thing about worms in the poop is that by the time they are passing enough worms in their poop to be noticeable they have a heavy infestation and all the internal damage that goes along with it. I don't know if worms are what's going on with your flock but that's certainly where I would...
Ridiculous that the vet wouldn't send in a fecal sample, or take a look at it under the microscope himself! I think I'd be finding a new vet that is more willing to be helpful.
What did you deworm them with last summer? I think what I would do is get a scissor and trim off all those fluffy...