This happens when .htaccess is used as the rewrite rule vehicle. I'm not aware of any workaround other than replacing ezurl/ezroot. But there shouldn't be too many instances on your user site, admin is a different story and I have not bothered removing the index.php from the path for admin access.
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So the difference would be that I am using an .htaccess file for rewrite at the hosting provider, but a modified httpd.conf on my local server? That would make sense, but I am sure that I would have never been able to figure that out...thanks for the help.