The fgets() function works differently when the input is a pipe.  Specifically, feof() returns true after the first line is read.  The test script and sample output follow.  The test script works fine if stdin is redirected from a file.  It fails if stdin is a pipe.

Nothing special about the build:

./configure  --prefix=/usr/local --with-mysql

pjm@poseidon> cat test.php 
#!/usr/local/bin/php -q
<?php

$fd = fopen("php://stdin", "r");
while (! feof($fd))
{
        $buffer = fgets($fd, 4096);
        echo $buffer;
}

?>
pjm@poseidon> < test.php ./test.php 
#!/usr/local/bin/php -q
<?php

$fd = fopen("php://stdin", "r");
while (! feof($fd))
{
        $buffer = fgets($fd, 4096);
        echo $buffer;
}

?>
pjm@poseidon> cat test.php | ./test.php 
#!/usr/local/bin/php -q