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If you are developing ANY applications under Projects in Developer Studio, the id that started the web application server is the id under which the files are created. We have WebSphere and it is always started under root. I worked with a different app server at my previous contract and it was root as well.
This has nothing to do with the id that starts the reporting server.
What you can try to do is, after creating the application directory from Projects or better yet create it from a Unix prompt or Data Servers (you can make it a project after), go to the Unix prompt and change the ownership to you and the permissions. To set the group sticky bit, do a chmod g+s on the directory.
I can't guarantee that will help but it can't hurt.