Color me confused. I am starting a project and have written 2.5 chapters totaling more than 4,000 words. All the chapters are included in the compile. Yet when I run Project Statistics, it lists Manuscript words as just 49 (and pages as 1). Not sure what I’m doing wrong. 
First things to check are that your documents are actually subdocuments of the Manuscript folder in the binder and that the compile settings are including text and not just compiling titles or such. For the former, click the disclosure triangle (or “+/-” button, if on XP) to the left of the Manuscript folder in the binder. If you still see your documents, they’re not currently contained in the Manuscript and therefore aren’t being included in the count. You can just select them and drag them into the Manuscript folder to move them, or use Ctrl-Up/Down/Right/Left.
To check your compile settings, click the blue arrow in the Compile dialog if necessary to see the left sidebar, then select “Formatting” and make sure that there are checkmarks in the “Text” column there. Project Statistics for the Manuscript (generally “Draft”) folder come directly from compile, so if you’ve set up to compile an outline of titles and synopses, say, that’s all that will get counted.
That was the problem. Thanks so much for the help!