This was one of the answers to the question why NDT might not work for some, and why a combination of synthetic T3 and T4 is sometimes preferable to NDT:
The problem with NDT is that the animal hormones are bound to thyroglobulin and unless that bound is broken the hormones are pretty much inactive. This gives the body a very easy way out if it doesn't want to increase metabolism for whatever reason.
When you take synthetic T4 and T3, you take 'free' hormones. They cannot be (very easily) inactivated.