The release notes for SQL Server 2005 SP2 indicate that seven issues were fixed with SSIS:
KB918644: The SQL Server Integration Services (SSIS) service does not start when you install SQL Server 2005 SP1 on a computer that is already running the SSIS service
KB920205: A memory leak may occur when you run SQL Server 2005 Integration Services packages that are stored in the SSIS Package store.
KB920882: You cannot deploy a SQL Server 2005 Integration Services package if you use an XML configuration file whose file name contains an uppercase letter.
KB922527: Error message when you schedule some SQL Server 2005 Integration Services packages to run as jobs: "Package has been cancelled"
KB924346: An access violation may intermittently occur when you run a SQL Server Integration Services package in SQL Server 2005.
KB928243: When you run a SQL Server 2005 Integration Services package, the package may stop responding.
KB928792: The output rows of the Aggregate transformation are divided into multiple rows in SQL Server 2005 Integration Services.
...so if you have any of those issues, then you may want to apply the appropriate hotfix.
It is also concerning that SSIS didn't get updated, because it begs the question "why not?" Often times if updates won't install, it is symptomatic of a larger underlying issue.
If you can, set up a "lab" environment and try to install the SP and see if you notice the same behavior. If not, you may want to consider doing a refresh of the SQL server installation or digging more into the root cause through installation logs etc.