(this helped me after manually compiling PHP 4.3.6, where phpMyAdmin, Horde Webmail, etc stopped working)
rm -f /usr/local/cpanel/cpanel /scripts/installgd /scripts/cleanmd5 /scripts/upcp
also... cPanel/WHM uses a buggy version for PHP (4.2.3) stricly for it's internal applications (e.g. phpMyAdmin)... to fix this simply delete that php version that it uses, and put an alias in it's place...
rm -rf /usr/local/cpanel/3rdparty/bin/php ln -s /usr/bin/php /usr/local/cpanel/3rdparty/bin/php