It sounds to me like a combination of two different scares we had.
The ServUO.exe
must be in the same directory/folder with the folders it needs to operate. One of these is "Saves". If a complete server save (including the all important "Accounts" file) is not in there, you will get the prompt to make an owner account. If this happens, stop the server immediately, saving nothing, and go find your latest valid save to copy into the proper "Saves" folder. BTW, make sure that your "server sitter" isn't using a desktop shortcut (pointing to the wrong files, of course) to start the server. Make sure that they go into the actual folder to double click the right file every time. Put it in a checklist.
BTW, not saying you did this, but if any files with the same names as "Saves" files are allowed to trash up your Server Master folder, the server gets confused and won't save properly.
The other problem is similar. The "Scripts" folder is missing some scripts for items listed in the "Items" file in the "Items" folder in the "Saves" folder, probably addons that the decoration staff has genned, but been slow in getting the scripts to the "server sitter" and other technical staff.
Whatever you do, make darned certain that you keep multiple valid current "Saves" copies (and copies of everything else) in multiple locations to use when something like this occurs. We send our saves, new scripts, and client patches to multiple locations via email daily, and synchronize our Development and Test servers with Production daily as well. The Foulup Fairy tends to stay away if she sees you're ready for her.