I went back in and tried it again. I got the same result. The log did not indicate that the ProjectComment.xml was processed either.
So I opened up the shfbproj file with an XML editor. I screwed myself on this one. I had created 2 DocumentationSources elements with conditions that allowed me to do a desktop build and a Team build from the same project.
I had used the SHFB GUI to add the ProjectComment.xml file. It shows up in the Documentation Sources panel. When I saved the project prior to the build, it put it in the section that would be selected if it were a team build. Since I was running it from
the desktop it never picked up the ProjectComment.xml. It built just like the project description was written.
Once again, you can chalk it up to user error. My apologies for wasting your time.