The SSIS Config file is called MsDtsSrvr.ini.xml. It is located in C:\Program Files\Microsoft SQL Server\90\DTS\Binn on my install.
I had to hunt it down as after installing Integration Services the service would not start.
It turned out that it didnt like the fact that I have named instances of SQL 2005 (no default instance) and SSIS doesnt detect named instances by default.
Adding the instance name inside the servername tags sorted my problem.
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