Just watching the video http://www.youtube.com/watch?v=Mg3KU8pkoEc. I see the shock issues are still there to some degree. Do you not have any shock viscosity term? I thought this would be essential, unless you go to a more involved (but much better physically) Godunov type scheme with an iterative Riemann solver.
It would also be interesting to see in addition to the density & temperature(s) evolution, the pressure, magnetic pressure and total pressure evolution (and plasma beta), as there are stages where across the shock it switches from high temperature/low density to low temp/higher density suggesting the shock in pressure is much weaker. This is also, I seem to remember, why a lot of codes use density and ion/electron pressure as their fundamental variables or even density and total energy, rather than density & temperatures.