Please try using this CVS snapshot:

  http://snaps.php.net/php5.2-latest.tar.gz
 
For Windows:

  http://windows.php.net/snapshots/

And what SAPI are you using? I guess CGI or FastCGI since there is no 
"native" SAPI for this odd webserver.

Tried with the latest CVS snapshot you attached, and the result is the same.

I am not working in CGI mode. As my web-server is apache like, it supports running php scripts natively. It links to the libphp5.so created after the installation of php and makes use of it directly.

What exactly is the configure line you used? Can you reproduce this 
problem using real Apache?

And you should really check what $output contains using this:

var_dump($output);

Here's the configure line used:
Configure Command =>  './configure'  
'--host=i686-linux' 
'--build=i686-linux' 
'--prefix=/usr/local' 
'--disable-all' 
'--enable-static' 
'--disable-shared' 
'--enable-memory-limit' 
'--disable-safe-mode' 
'--disable-rpath' 
'--disable-ipv6' 
'--disable-wddx' 
'--disable-bcmath' 
'--enable-debug' 
'--disable-calendar' 
'--enable-ftp' 
'--without-aolserver' 
'--without-apache' 
'--without-continuity' 
'--without-pi3web' 
'--enable-releasemode' 
'--enable-xml' 
'--cache-file=config.cache' 
'--enable-libxml' 
'--with-libxml-dir=/usr/local' 
'--disable-simplexml' 
'--enable-dom' 
'--enable-soap' 
'--with-db' 
'--enable-sockets' 
'--enable-track-vars' 
'--enable-trans-sid' 
'--enable-magic-quotes' 
'--without-pear' 
'--with-zlib' 
'--with-exec-dir=/usr/local/appweb' 
'--sysconfdir=/usr/local/appweb' 
'--with-gnu-ld' 
'--with-openssl=/usr' 
'--enable-mbstring' 
'--disable-mbregex' 
'--enable-session' 
'--enable-pcntl' 
'--enable-pdo' 
'--with-pdo-sqlite=/usr/local' 
'--with-pcre-regex' 
'--enable-spl' 
'--enable-tokenizer' 
'--with-snmp=/usr/local' 
'--enable-ctype' 
'--enable-apc' 
'--with-ctype' 
'--without-tsrm-pthreads' 
'--disable-threadsafe' 
'--disable-maintainer-zts' 
'--enable-embed=shared' 
'--enable-cgi' 
'--enable-cli' 
'--enable-inline-optimization' 
'--with-curl=/usr/local' 
'--with-curlwrappers' 
'--enable-cipher'

1. I tried using "var_dump()" - got the same results.
(it prints "int(-1)" all the time).

2. regarding the apache server - I don't have one installed/configured on my system but I will give it a try.

Another important comment - The funny thing is that the command finishes succesfuly!

I tried using a small c program that I wrote:
#include <stdio.h>
int main(int argc, char **argv)
{
        printf("true was called!");

        return 0;
}

So when printing the $output var, it holds the correct string. It is just the $status var that holds the wrong value.

First of all: You're obviously running PHP as CGI since that's the only one you're compiling with that configure line. Also, try this script instead:

<?php
for ($i = 0; $i < 10; ++$i) {
  exec("/bin/true", $out, $status);
  var_dump($out, $status);
  exec("/bin/false", $out, $status);
  var_dump($out, $status);
}
?>

1. Here's the output of your script:
array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) array(0) { } int(-1) 

2. Regarding the CGI mode. Maybe I don't understand the concept of CGI well enough - I will try to explain my setting:
a. I compile php and create the libphp5.so. Notice the "'--enable-embed=shared'" directive in the configure line.
b. I compile my web-server (appWeb). It has an internal module for running php scripts which dynamically links to the libphp5.so.
Is this referred to as CGI mode or SAPI mode?

Hi,

Tried with the latest version of apache2 and it works OK.
Something with the mode I am using is wrong. Do you have any ideas? Are you familiar with such errors maybe?

There's something wrong with your webserver. This is in no way any PHP bug.