had problem on two computers (so far, we're just started) with our custom TVHost 12 installation.
1. on Windows 10 Pro x64 under domain admin, I had no rights on AssignmentData.json file in TV installation folder.
2. on Windows 7 Pro x86 under domain admin, "Administrators" group had only read rights on AssignmentData.json file.
In both cases I didn't see custom logo and naturally could not use autoassign tool because it needs to access this file.
I fixed (inherited) access rights on TV installation folder, restarted TV, assigned with the tool, all was fine.