I see. That variable inductor could be the problem for VHIL/real-time simulation. It's under the hood implementation differs for these two different platforms. In TyphoonSim we can simply change inductance value, reinitialize solver and continue since it is variable step offline simulation. In real-time (as well as in VHIL that is emulator of the real device) variable inductor is implemented as controlled current source in order to make it possible to run in real-time. Hence, depending on parameters of the entire circuit where such variable inductor is involved, circuit can become unstable due to variable inductor.
I would suggest you to run one simulation with regular inductors with some value from your test case. If that works, problem is identified and you can start looking for solution.
One of them would be to reduce simulation step for VHIL. You mentioned that in TyphoonSim you are using max sim step 1e-6. But that is maximal simulation step allowed for solver. If needed solver can reduce it to order of picoseconds for example, because it is variable step solver. On the other hand, VHIL uses discrete step and you selected 1e-6. In general, smaller step should give you better results, so I would advise reducing simulation step for VHIL (real-time).