I am having problems with X3 not saving my meter settings (i.e. RMS + peak) plus the horizontal meter preference for the track view.  This is a very specific repeatable problem. Has anyone else had this issue and possibly found a workaround?

There was a long-standing issue with Record meters not persisting the Peak+RMS mode, but that actually finally got fixed in one of the releases of X3. I just checked persistence of this mode for all metering options (Inspector options are separate from tracks), and they all seem to be saving successfully. I haven't seen a problem saving the orientation, either. Do you have the X3d patch installed?