You may want to give the PDF review a look: I Came, I Saw, I Learned...: Adobe RoboHelp 9: PDF Review
For the Word file, did you include all topics you want in the output settings? Printed documenation works different from web outputs in that you need to select all topics you want to include.
The Word output window has several screens that you can move through. (The .CHM output only has one window.) Instead of choosing Save and Generate, choose Next. In the second screen, choose the double arrows pointing to the left to remove all of the topics and then either choose the double arrows to add all of the topics back OR just include the sections that you want reviewed. If you've conditioned out specific topics BUT you add the topics, they will show in the Word document. Conditioned text within a topic won't display.
Note that my screenshots are from RH10.
Thanks. Found it after I posted (which I deleted). Never noticed the Next button before as I've only generated Web and CHM outputs. Thanks to all.