It may be that you have not selected a top-level VI for your application. The LabVIEW 6i Application Builder can include all of your (non-dynamically loaded) subVIs for you automatically, just based on telling it what your top-level VI is. I thought the Application Builder would check for that automatically, but apparently it doesn't.
For help with the Application Builder, I recommend the LabVIEW Application Builder Troubleshooting Wizard in the National Instruments Support site. You can get there by going to http://www.ni.com/support and then choosing "LabVIEW" from the list of products. That will take you to the main LabVIEW Support page (http://www.ni.com/support/lvsupp.htm). From there, choose the link to the "Application Builder Troubleshooting Wizard". That p
age has version-specific Application Builder help for LabVIEW 5.0, 5.1, and 6.0.
Regards,
Mr. KB