I've never had a problem with the particular folder/directory in particular you mention with a linux apache php or cgi php setup. If this is the case contact your host and have them reset the folder. It's your hosting account they will have no problem with that and it's a relatively simple task for them.

Before you do, you might look around a few other folders/directories and make sure you don't have a few other nobody's or 99's that you might want to tell them about too.