The script is different from what's used on unixes.
It was not playing the table insertion script (mysql_system_tables_data.sql),
although it was checking for the presence of this script.
Fixed by re-enabling the lookup for this file and replaying it at bootstrap
time. Note that on the Unixes "SELECT @@hostname" does return a fully qualified
name, whereas on Windows it returns only a hostname.
So by default we're filtering records in the mysql.user table until we ensure
this is fixed.