Kevin, are you sure your site_url and site_index values are set properly? Publisher uses those values when determining how to handle segments. As long as the first segment, caehc, is in the config, it is removed with the domain name when Publisher does its url magic, so it shouldn’t be causing an issue like this.

I won’t be able to try to replicate this locally until this weekend, but this should work. https://screenshots.firefox.com/VuDG2cEtyvGgmKTM/ee400.vm

I moved a dev site into a sub folder and I wasn’t able to replicate this. I tried it using .htaccess to remove the index.php from the url, and then forcing index.php into the url and it still worked fine. I’m pretty sure this is still a config issue on your site. Have you tried htaccess to remove index.php from the url? I can’t login to your CP, but the front-end of your site is adding index.php, is that intended? If so, make sure EE is setup so the site_index has index.php in it. If its not intended, change your config and use htaccess to remove index.php from the url.