and the contour plot appears as I would expect it to.
I may look similar to what you expect, but I doubt its correct. Make the contour plot a surface plot and then plot the same three vectors as scatter plot (this time you see the single points). You will notice that the points are not on the surface plotted. So the surface probably is not the exact surface you want the contourplot be plotted of.
We had a similar probleme here a while ago http://communities.ptc.com/message/244950#244950
You might find that thread useful for your problem, too.