After we did a migration from an earlier version of SQL to a new server we needed to rename the Windows server to match the old one.
It does actually seem to rename the SQL instance when you open SQL SSME but there is an extra step to complete fully:
Run the following in Query Analyser:
Which will return the old name of your SQL Server
Then using the quotes if needed (esp if your server name includes a hyphen) :
sp_dropserver ‘old server name’
sp_addserver ‘new server name’, ‘local’
Run SELECT @@SERVERNAME again should return the name of the correct server