When I run things in JMS, such as create a new slave site or patch files, the new/changed files now have ownership of wwwrun instead of the original ownership. Because I don't have root access on our server, I'm unable to chown these files to the proper owner and I have to ask our server admin to do it. Is there a way to stop JMS from chown on any files it creates or changes?

Contact your hosting provider that does not provided you a correct environment that manage correctly the ownership of the files and folders.

In general, the hosting providers use suPHP apache module to guarantee that the files and folders have correct ownership. This suPHP apache module use the owner of the files that is executed (here probably index.php ownership)

What you describe is that your hosting provider provide another ownership than the FTP account that you used to install your Joomla.

Thanks. We don't use a hosting service -- we have our own servers. So I'll contact my server admin and have him look into this.