I found out what was wrong.
With the manual method you have to start a script (make_bootable_linux or make_bootable_mac). Off course you should give this script the attribute +x, so it can be executed. The script does some checks and then copies files to the USB-drive. One of the last steps in the script is a 'call' to an other script: /tmp/UNRAID/syslinux/make_bootable_linux.sh. The problem with this is, that the script is just copied and does not have an execution flag (+x). After I've added the command "sudo chmod +x /tmp/UNRAID/syslinux/make_bootable_linux.sh" it works if I start the script with an unmounted (but plugged in) USB.