IBM Secure Diagnostic Data Upload Utility stores it's settings in the file ibmsdduu.conf. This file is created in the home directory of the user.
Example: userid paul - Config file: C:\Documents and Settings\Paul\ibmsdduu.conf for an Windows XP system.
It is possible to change the name and location of this file. This is controled with the command line option -config=file.
Example: -config=C:\temp\ibmsdduu.conf