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After running the server_diag_tool, the following error message is returned:
"[Fatal Error] Server.dat:42:1: XML document structures must start and end within the same entity.
ArcGIS Server Machines
(1) server.domain.com (SOM,SOC)
The '<arcgis_dir>/server/system/Server.dat' file is missing its closing '</Server>' tag.
In rare cases, this issue has been reported upon upgrading ArcGIS Server Java from 9.3 Service Pack 1 to version 9.3.1.
Add the closing '</Server>' tag within the '<arcgis_dir>/server/system/Server.dat' file.