Kudos to TYM for doing the right thing, but it sounds like there is a design issue, they are aware of it, and they are eating it. Even if it is good business, they can't cover repairs 3 years out of warranty and stay in business- unless they have a serious issue to deal with. Like Toyota and frame rot. There is a design issue with the tractor, and if they are replacing your frame with a used one, you had better check it over REAL well- it could have stress cracks or breaks like your original frame. At the least, before it is installed, that would be a good time to reinforce it. But, they may not be willing to do that, or any alteration to the frame may void any warranty. Which brings up the next question- if they are installing a used frame, do they warranty it?
A tractor is designed to work. The front axle pivots- even when the loader is full and heavy, one wheel higher than the other doesn't add (it definitely shouldn't add undue stress, or it is poorly designed) to the frame unless the axle is pivoted so steeply that it is resting on the stops, and you are putting more stress on one side than the other. Even then, the frame should be able to take that. If it doesn't, then it shouldn't be sold. If the loader will lift it, the frame and other components should be able to more than handle it.
If the frame is 3/8" at a strategic point, and this is happening to multiple tractors, it is pretty obvious that there is a design flaw. Replacing it with the same frame will only buy some time.