Hi Jehlojj,
Yes, I found that there was left over 'folder structure' from the previous version of OS X which Server 5.2 was not understanding.
How I fixed the problem:
First I re-downloaded Sierra and created a bootable USB flash disk (8Gb), you can follow the instructions here: Create a bootable installer for OS X - Apple Support - it is a bit technical but if you follow the Path for El Capitan (obviously replacing El Capitan with Sierra in terminal).
e.g. (please double check the code for yourself!)
sudo /Applications/Install\ macOS\ Sierra.app/Contents/Resources/createinstallmedia --volume /Volumes/MyVolume --applicationpath /Applications/Install\ macOS\ Sierra.app
The process does take a while to copy but worked perfectly - from there you can redownload Server and it sets up as normal 🙂
Please let me know if this sorts out your problem too