This may help. I had the same problem i think. I could access the plain site but none of the links would work, the admin site i couldn't access. I found out that my php install is running as a cgi and if I wanted to run it as an apache module i need to create and .htaccess file and put in it: RemoveHandler .php. the .htaccess file had to be placed in my home directory. It now works perfectly.