When you run into this problem, just allow your device to complete the first boot. There may be still a background process being busy executing cloud-init and the Ubuntu user hasn't been created yet.
For, just trying again after more wait time fixed the issue.
I found the solution myself.
The trick is: linking the the two folders by a symbolic link
Opening terminal from within the "files" folder (/var/www/html/files on the Pi), and type:
sudo ln -s /media/usb1
(I was running pmount to automount and allocate name usb1 to any usb attached to Pi.