To run a shell script with all the variables that you would have when logged in interactively add bash -l or sh --login infront of your command. The script I use creates a shell script, copies the script to the box with ssh2_scp_send, then executes the script with ssh2_exec. Hope this helps somebody.
<?php
$script1 = "bash -l /etc/rc.d/rc.httpd restart";
$connection = ssh2_connect('shell.example.com', 22);
ssh2_auth_password($connection, 'username', 'password');
$stream = ssh2_exec($connection, $script1);
?>
