Works fine for me (and there weren't any changes between 5.0.3 and 5.0.4 which could have broken it). There's just something wrong with your system. (check config.log, there you most likely will find the reason the check failed)

Also: paths like /usr/lib do NOT WORK! (they never did and they never will, drop the /lib part from those!)

Okay I have compiled php-5.0.3 and php-5.0.4 with the configure options.

 ./configure --with-gd --with-mysql=/usr/local/mysql --with-apxs2=/usr/local/apache2/bin/apxs --enable-track-vars --with-pspell --with-memcache --enable-soap --enable-exif --with-tidy --with-curl --with-png-dir=/usr/local --with-zlib-dir=/usr --enable-force-cgi-redirect --with-gettext --with-freetype-dir=/usr/local --with-jpeg-dir=/usr/local

I have tested the script below on the command line.

# cat ../imagecheck.php
<?php
        $func_name = "imagecreatefromjpeg";
        if(function_exists($func_name))
                echo "Function $func_name exists\n";
        else
                echo "Function $func_name does not exist\n";
?>

With php-5.0.3

# ./sapi/cli/php ../imagecheck.php
Function imagecreatefromjpeg exists

With php-5.0.4

# ./sapi/cli/php ../imagecheck.php
Function imagecreatefromjpeg does not exist

If there was a problem with the system and nothing had changed between the versions then the same problem would occur in php-5.0.3

I downloaded the source again and did a difference check

# diff -Naur php-5.0.4old php-5.0.4new > php.diff

There were differences (apart from generated files by configure, make etc) so I compiled again with the newly downloaded source and everything has worked fine. Obviously not a problem with my system then!