[wp-hackers] Interesting Permalink Issue

[Jeffrey Nolte]

Hello,

When going to the permalinks section in wp-admin the links are all prepended with index.php like so.  
When selecting any of the permalink settings it does not work at all and we get 404 on most pages.  The only way the site site will work is with the default permalink settings.

Does anyone have an idea of what this could be or how to begin debugging?

Thanks in advance,

Jeffrey Nolte