Hi Div -- I work for Sonnet, Sonnet at least (perhaps the others too) has no problem with lossy/conducting substrates. When loss is added, analysis time increases, but there is absolutely no change in accuracy.
If you network is not too big, you can use the free SonnetLite,
www.sonnetsoftware.com.
If your network is planar (even including thick metal) should not use a volume meshing code, definately use a surface mesher like Sonnet (shielded analysis) or Momentum (unshielded analysis).
If your circuit has any non-planar aspect, or you want to get a second analysis using a different approach as a check, then I recommend CST. We evaluated CST extensively against all competitors (accuracy, quality of solution, speed, and user interface were the primary criteria) before my company decided it was very much worth it to repersent it in North America.
If you wish to check any EM analysis for accuracy for conducting substrate I suggesting analyzing a parallel plate capacitor. Set the conductivity of the dielectric to a known value. Calculate the resistance you should have. Then see if that is the resistance you get when you analyze it. If conducting (or lossy) substrate is important, you should definately do this test no matter what EM analysis you are using.