THX for this post. I've got a similar situation, but not nearly the amount of 'shudder' you describe. I have not really broken the brakes in properly, as the fellow from Tekonsha described (which is really how the Prodigy owners manual describes testing and setting the level of boost for the rig.) We did put about 1500 miles on it in Sept and I do still have just a bit of shudder only at low speeds, as you would if your vehicle has new rotors or has set for some time and had the rotors rust up a bit. I figured I just need to hit them hard a few times, so this sounds like what I'll have to do in spring.
Otherwise, I agree with ArizAl that if that does not cure it, make the dealer take care of it. Its a new trailer, that's what you pay for, even if the dealers don't like it!
Fred n' Jeri
2012 FF X-214WSD
2010 RAM 1500 Crew Cab 4x4, 5.7 Hemi MDS, Huskey 1200lb trunnion WD, Prodigy Brake
Prion Seayak Kayaks