If you have multiple SQL Server instances on a server, running the service pack install in ‘default gui’ mode will only apply to the default instance. To install to all instances at the same time, you need to expand the service pack, then run from the command line with the /allinstances tag: [more]
http://www.sqlserverclub.com/articles/how-to-upgrade-sql-server-instances-quickly-and-quietly.aspx
Here is some related info on SQL instances from MSDN:
http://msdn.microsoft.com/en-us/library/ms143531(SQL.90).aspx