Parallels

When previewing the site, all of the hyperlinks on the pages work. However, when the site is published, all of the hyperlinks in the menus work, but the hyperlinks in the body of the pages don't. Looking more closely at the problem, I can see that when in preview mode, all pages are .php files (e.g. page1.php). However when the site is published, all pages are uploaded as .html files (e.g. page1.html). When the site is published, the hyperlinks in the menu are being changed to point to page1.html instead of page1.php, however, the hyperlinks in the main body of the pages are being left pointing to page1.php (which does not exist). I've tried deleting and re-creating the links, and I've tried deleting the published site and re-publishing but this still doesn't work. Is there any fix for this?