I think I am getting the same problem. I may be acting like a complete noob, cause I've never worked with .htaccess files before, but in order to solve the register globals on security alert in protector, i need to make a .htaccess file in my main site root, and put
"php_flag register_globals off " (without the quotes) in it? I did that, and I got the same server error. It might be because I never set up .htaccess users or anything though?(If you have to?) I just installed this module today, the newest version.