I created a child them per instructions here

http://docs.orchardproject.net/Documentation/Customizing-the-default-theme

I then made changes to the site.css file using VS 2010. My new theme also has an alternate view file named
Parts-Title-MyPart.cshtml

Then from a orchard command line I issue the command

package create MyNewTheme c:\temp and a .nupkg file is created.

(Initially I got an error message "Cannot create a package that has no dependencies nor content", but when I changed the Theme.txt Version from 130130 to 0.9 it generated the nupkg file)

I then ran WebMatrix and generated a new Orchard Website and installed the nupkg theme and set it to current theme.

The problem is the site.css and the cshtml files from my new theme are not included in the ngpkg file. Am I doing something wrong?

Are you editing site.css in The Theme Machine and not using a css file in MyNewTheme?

Just the opposite. I am editing the site.css in MyNewTheme and leaving the site.css in The Theme Machine alone. I assumed the files under the child theme would override the filed in the parent theme.