What operating system are you using? And how do you know the directories "do not get a user or group assigned?" If you are using Unix or Linux, and ls -l reports user and group as "nobody," that is perfectly normal. "Nobody" is a user:
$ finger nobody
Login: nobody Name: Nobody
Directory: / Shell: /bin/sh
Never logged in.
No mail.
No Plan.
... specifically, a special user account of a fake user that is not allowed to log in, or have shell access. Running the Web server as "nobody/nobody" is a normal security precaution.
The superuser should be able to change the uid/gid/permissions of files created by the Web server.
