When the Software Vulnerability Agent is installed and running as a service, you may see a white list added in the scan agent log that does not appear when running agent scan manually using the command line.
[12/03 11:39:23.899] Append in whiteList path = D:\TEST
[12/03 11:39:23.023] : Initializing Filesystem Inspector
[12/03 11:39:24.052] Added "C:\" to search list
[12/03 11:39:24.073] Added "D:\" to search list
[12/03 11:39:24.099] Skipping "C:\" from the scan, since it is not allowed.
If there is no white list configured on the server, you need to check two local locations and make sure there are no rules.json file present.
When scan is running as a service it uses rules.json from below location
Executing Software Vulnerability Manager Agent scan manually will use below location for rules.json file
%LocalAppdata%\Vulnerable Software Discovery Tool
Deleting rules.json should correct issue with data not showing or scan results differ between scan executed manually in command line and automatically by the Flexera Corporate Software Inspector Agent service.