A few weeks back I published a post called Security patching can make you LESS Secure! Redux which reports that upgrading your 10.2.0.3 Oracle database to 10.2.0.4 causes the WKSYS password to be reset to the default value and _trace_files_public to become unset, meaning set to TRUE.
A little more research revealed that the problem lies in the Database Upgrade Assistant or DBUA. If you perform a manual upgrade, neither of the above two issues occurs. The bottom line is that you should never run a blackbox 'assistant' when you can simply run a few scripts. Who knows what that blackbox is doing. In this case, the only thing the DBUA 'assisted' with was making your database less secure.
The manual upgrade is easy and fully documented in the patch readme. After installing the software simply:
SQL> STARTUP UPGRADE
SQL> SPOOL patch.log
SQL> @?/rdbms/admin/catupgrd.sql
SQL> SPOOL OFF
Review the patch.log for issues and then:
SQL> SHUTDOWN IMMEDIATE
SQL> STARTUP
SQL> @?/rdbms/admin/utlrp.sql
You should not need DBUA for these simple tasks.
By the same logic you should consider not running DBCA, the Database Creation Assistant or allow the installer to create a database for you. This is easily scripted for most databases.