Can u tell us exact your server configuration?
apache version, php, mysql.
have u tryed see how much processor loads when u open your site?
I just tryed update my php version 4.2.3 to 4.3 and many scripts start loading processor to 100% and some scripts getting error...
another thing that I had experienced simular to your problem was that I didnt set correctly MySQL and it coundn't correctly detect what IP is my machine, so it was working very slow to.
maybe your case is something else...