Good point - I should have clarified this.
The DNN File Manager starts at a lower level than your FTP program. For example, in my installation I have the directory structure:
/httpdocs/Portals/0/
But to the File Manager, it considers this the "Portal Root". So if you want to see a file in the File Manager (and everywhere else), it must be stored at the level "/httpdocs/Portals/0/" or lower.
For example, if you see a directory "/Portal Root/images/" in File Manager, it actually will look like this to your FTP program:
/httpdocs/Portals/0/images/
Anything you store above "/httpdocs/Portals/0/" will be invisible to File Manager. If you create a directory:
/httpdocs/images/
File Manager will never see it.