When I simulated a basic design of two materials with a thin sheet of thermal insulating material in between them. There was no difference in temperature if I hadn't have put the TIM in it.
Is this correctly modelling it or are there betters ways to introduce TIMs into a simulation?
I'm not sure what your setup is so its hard to say what may be going on, but make sure that you have a thickness of at least 2-3 nodes to get accurate results