I took a look at your model and think this is a multi-layered issue. You should first isolate the electrical system and make sure that you are satisfied with its operation, including at steady-state. I don't believe the waveforms all look at you might expect, for example the output current. You may need to add damping, or general adjust the output voltage source/inductance values. Also, the phase b inductance doesn't match the other 2 phases. Once your electrical circuit performs correctly, you can add the thermal model and check that that works properly.