Weird ioctl behaviour in a linux program called using system()

Hello, I have a C program that allows setting a custom baud rate on a serial device.

It uses ioctl() to do so under linux, but its behavior is different when I use it under matlab, compared to a standard invocation from my terminal.

set_baud.c

#include <stdio.h>
#include <fcntl.h>
#include <errno.h>
#include <stdlib.h>
#include <unistd.h>
#include <stropts.h>
#include <asm/termios.h>

int main(int argc, char* argv[]) {

    if (argc != 2) {
        printf("Usage: %s <serial device>", argv[0]);
        return 1;
    }

    int fd = open(argv[1], O_RDWR);
    int speed = 31250;

    struct termios2 tio;
    ioctl(fd, TCGETS2, &tio);
    tio.c_cflag &= ~CBAUD;
    tio.c_cflag |= BOTHER;
    tio.c_ispeed = speed;
    tio.c_ospeed = speed;
    int r = ioctl(fd, TCSETS2, &tio);
    close(fd);

    return r;
}

relevant matlab line

serial_port = '/dev/ttyUSB1';
system('gcc set_baud.c -o set_baud');
system(['./set_baud ' serial_port]);

When calling it from matlab, a baud rate of 38400 (which is a default baud rate) is set, while calling it from my terminal sets the correct one.

I still have to run strace to it, is anybody aware of a reason for this?