To ensure that all the files in the File Manifest Source Directory are actually included in the File Manifests use Validate File Manifest(s).
Click "Validate File Manifest(s)" on the main toolbar or main tree view context menu:
File Manifests that do not contain all the files in their Source Directory will appear red:
Modify affected File Manifests and check the Status Bar. Click "Refresh Files From Source Directory". The Status Bar shows a count of how many files are in the File Manifest and how many files are in the Source Directory:
If it is necessary to clear all existing files from the File Manifest click "Yes", if not, click "No" when prompted:
Add any missing files to the File Manifest by clicking the relevant file's checkbox: