Magento

Hi I am running 1.1.6 and when I activate web server rewrites the header links can’t be found I have shared SSL and if I tun it off I get those links back I need to enable rewrites because that solves the “index.php/” issue that I have.(if I click on the logo it takes me to www.mydomain.com/index.php/, which blocks the content on main page and most of the static blocks don’t work
Please help

thanks