I have just installed the plugin and it seems to run well except that I have a custom html module in place of a standard joomla menu. The module has graphic buttons that use the html href command to link to pages on the site. The problem is that now none of those buttons work. this is what the url looks like when you try to go to a page

www.mysite.com/index.phpcomponent/content/

instead of www.mysite.com/my-page

Please help!
Thanks