Hi
You could check the following things:
1. Have you checked to see whether all the SQL services on each instance is running or vice versa. IE try running the hotfix when all SQL services are stopped, and then try again when all are running. Start and stop the services on SQL Server Configuration Mgr.
2. Run FileMon to see which processes are using the atx90 dll. Stop that process on TaskManager or the services console
3. If you are running 64bit SQL, make sure you download the appropriate hotfix for your version.
Good luck