Diesel Bombers - Reman NV5600 issues

I recently had a reman NV5600 put in my truck. Truck is a 2000 so it had the 1 1/4" input shaft. I had everything swapped over to accommodate the newer style 1 3/8" input shaft. I have only put around 100 miles on the truck since the trans work was done. I have a nasty grind going into 4,5,6 and it won't downshift at all without grinding something fierce. I took it back to the shop yesterday and had the guy drive it and he said that something is definitely wrong. He called the supplier and told him about the issues I am having and the supplier told the mechanic that I need to put more miles on it and that the reman trans won't be broke in and stop grinding for atleast 1000 miles. Does this sound fishy to anyone else? I have a warranty on the trans and was hoping that they would just swap it out, but the supplier said that another trans would just do the same thing until I put some miles on it and that he doesn't have any cores that he could use to build a new one with for a couple of weeks. Has anyone else ran into this with a reman? My initial impression is that the guy is feeding me a line of bull.