I had fixed my issue which sounded very simular.
After the Install of SP3 CU9 or in my case SP4 I combed the logs and found errors copying DTS perf ini files which were corrupt.
1) Program Files\Microsoft SQL Server (x86)\90\DTS\perf-DTSPERF.INI
2) Program Files\Microsoft SQL Server\90\DTS\Binn\perf-MSSQLSERVERDTSPERF.INI
I deleted the above files a recreated them with the contents from:
1) Program Files\Microsoft SQL Server (x86)\90\DTS\DTSPERF.INI
2) Program Files\Microsoft SQL Server\90\DTS\Binn\DTSPERF.INI
peer the corresponding numbers with files
Rerun the service pack again, maybe unique to my situation
Good luck