>У меня идеи потихоньку заканчиваются - не взыщите. Из безумных вот:
>
>1. Апач случайно не в chroot'е работает?
>
>2. Не запускает ли он PHP в Safe mode? Если так, то
>что указано в safe_mode_exec_dir в php.ini?
>
>3. Ваша программа comonn чувствительна ли к пользователю, который её запускает? Может,
>если её запустит апачевский юзер, то она ведёт себя как-то не
>так?

Не chroot ..

Apache 2.2.
PHP 5.5.
FreeBSD 6.1-RELEASE #0

php.ini :

///////////////////////////////////////////////////cut
safe_mode = Off

; By default, Safe Mode does a UID compare check when
; opening files. If you want to relax this to a GID compare,
; then turn on safe_mode_gid.
safe_mode_gid = Off

; When safe_mode is on, UID/GID checks are bypassed when
; including files from this directory and its subdirectories.
; (directory must also be in include_path or full path must
; be used when including)
safe_mode_include_dir =

; will be allowed to be executed via the exec family of functions.
safe_mode_exec_dir =
; When safe_mode is on, only executables located in the safe_mode_exec_dir
; will be allowed to be executed via the exec family of functions.
safe_mode_exec_dir =

; Setting certain environment variables may be a potential security breach.
; This directive contains a comma-delimited list of prefixes.  In Safe Mode,
; the user may only alter environment variables whose names begin with the
; prefixes supplied here.  By default, users will only be able to set
; environment variables that begin with PHP_ (e.g. PHP_FOO=BAR).
;
; Note:  If this directive is empty, PHP will let the user modify ANY
; environment variable!
safe_mode_allowed_env_vars = PHP_

; This directive contains a comma-delimited list of environment variables that
; the end user won't be able to change using putenv().  These variables will be
; protected even if safe_mode_allowed_env_vars is set to allow to change them.
safe_mode_protected_env_vars = LD_LIBRARY_PATH
///////////////////////////////////////////////////cut

Программа скомпиленная GCC: (comonn) (посылает пакеты из 8 байт в СОМ порт - на входе последовательность пакетов по три символа, программа обрамляет пакеты приставкой и окончанием:

/*
        *       gcc -O2 -o /test/COM/com /test/COM/com.c
        */

        #include <stdio.h>   /* Standard input/output definitions */
        #include <string.h>  /* String function definitions */
        #include <unistd.h>  /* UNIX standard function definitions */
        #include <fcntl.h>   /* File control definitions */
        #include <errno.h>   /* Error number definitions */
        #include <termios.h> /* POSIX terminal control definitions */
        #include <locale.h>

        #define MAXL 255                /* макс. длина строки */

        /*
        * 'open_port()' - Open serial port 1.
        *
        * Returns the file descriptor on success or -1 on error.
        */

int open_port(void)
        {
        int fd;                         /* File descriptor for the port */
        struct termios options;

        fd = open("/dev/cuad0", O_RDWR | O_NOCTTY | O_NDELAY);
        if (fd == -1)
                {
                /*
                * Could not open the port.
                */
                perror("open_port: Unable to open /dev/cuad0 :( ");
                }
        else
        {
        fcntl(fd, F_SETFL, 0);
        printf ("Port OPEN OK!:>\n");
        }

        tcgetattr(fd, &options);
        cfsetispeed(&options, B57600);
        cfsetospeed(&options, B57600);
        tcsetattr(fd, TCSANOW, &options);

        return (fd);
}

int main (argc, argv)  char **argv;
        {
        int fdd;
        int n;
        char str[10];

        printf("\n^^^^^^^^^^^^^^^^^^^^^^^^^^\n|    (c) Termsl' 2007    |\n-------------------------\n");

        fdd = open_port();
        setlocale(LC_ALL, "");
        if( argc == 1 )
                {

                                        /* программа вызвана без аргументов */
                }else{                  /* аргументы программы - имена файлов */

                while( argv[ 1 ] )
                {
                printf("<%s> ",argv[1]);
                n = write(fdd," <!",3);
                n = write(fdd,argv[1], 8);
                n = write(fdd,"> ",2);

                argv++;
                argc--;
                }
        }
        if (n < 0) fputs("write() failed!\n", stderr);
        close(fdd);
        printf ("\n<: Port CLOSED OK! \n=========================\n\n");

        exit(0);
}

собирал под root, потом:

положил comonn в / сделал
chmod 0777 /comonn
chown www /comon

в index.php поменял пути .... таже ерунда
также клал в одну папку s index.php....