This is a design limitation of FastCGI. Since you are running PHP in CGI mode, it cannot get variables and other things from .htaccess anymore.
If you switch back to mod_php mode, it should again start recognizing .htaccess variables for php.ini settings (and others).
NOTE: The Fast-CGI does not affect things like mod_rewrite commands in .htaccess, only PHP related commands.
-Will
P.S. You don't get any performance benifit out of using FastCGI over mod_php. FastCGI is significantly slower than mod_php. You may get a slight security boost, but that is also debatable.