script creating root files

i have a script which creates directories that belong to root. the problem is, my apache is running as nobody, nobody is set in the httpd.conf, and nobody exist in my /etc/passwd. however, whenever i run a the php script to mkdir or upload a file from my HD to the server, or copy files from one location to another server on the server, the resulting file or directory belongs to root. ls -al shows root.root as the owner of the file. anyone know why? i thought all files created by the script should be nobody.nobody, but somehow all the scripts on this particular server creates root.root files and directories. any idea how to solve this? regards