Running fork, dup2 and exec from a C program in background - c

Question

I'm developing a embedded C application (gather.out) for a controller that runs Debian 8 (Jessie). This application calls another program called gather. The gather program prints some data on screen when I run it alone on the terminal. I decided to use fork and dup2 to redirect the output to a output file that contains the gathered data, as follows:
pid_t pid=fork();
/* Child process */
if(pid==0)
{
// Open gather output file
int gather_file_fd=open(actual_filename, O_WRONLY | O_CREAT, 0777);
if(gather_file_fd==-1)
{
return 2;
}
// Make stdout of gather program as input of output gather file
int gather_file_fd_dup=dup2(gather_file_fd, STDOUT_FILENO);
// Run the gather program
int err;
err=execl("/usr/bin/gather","gather","-w",NULL);
if(err==-1)
{
return 2;
}
}
Everything goes fine when I run it from the terminal, manually. When I set the controller to run it as startup (I don't know exactly how the controller start the program on boot, but it does) my output file gets corrupted.
I don't know how to debug this problem but I was trying to see the TTY of the processes to have some idea about what's happening using ps ux | grep gather. When running manually:
# ps ux | grep gather
root 18014 49.4 0.3 219380 6240 pts/0 RLl+ 14:50 0:51 ./gather.out
root 18022 39.2 0.2 219304 5988 pts/0 RLl+ 14:52 0:01 gather -w
root 18026 0.0 0.0 2076 568 pts/22 S+ 14:52 0:00 grep gather
And running at startup:
# ps ux | grep gather
root 17859 80.5 0.3 219380 6240 ? RLl 14:42 0:33 /var/ftp/usrflash/Project/C Language/Background Programs/gather.out
root 17978 45.0 0.2 219304 5984 ? RLl 14:43 0:01 gather -w
root 17982 0.0 0.0 2076 532 pts/0 S+ 14:43 0:00 grep gather
From there I noticed that there is no TTY attached to the processes running the program at startup. Does it affect the way I redirect the output with fork, dup2 and execl?
Edit 1
The correct output file must be like this (produced by gather application, runing gather -w > /var/ftp/gather/test.txt on the terminal and start the data acquisition on controller's IDE):
Waiting to gather
0 0 0
0 0 0
0 0 0
...
Where each line 0 0 0 is the sampled signals from the controller and could be any value, the ... indicates that the file is very large. When I run the gather program on the terminal gather -w > /var/ftp/gather/test.txt &, start data acquisition on controller's IDE, the gather program suddenly stops when I hit enter on terminal:
# gather -w > /var/ftp/gather/test.txt &
[2] 22232
#
[2]+ Stopped gather -w > /var/ftp/gather/test.txt
#
And the output file prints just the header:
Waiting to gather
Starting the gather program in background using gather -w < /dev/null >& /var/ftp/gather/test.txt & as one of the comments' advices and starting the data acquisition on controller's IDE I got the following file output:
Waiting to gather
Waiting to gather
Waiting to gather
Waiting to gather
...
The number of lines on the file is much greater than the number of samples on sample counter watched by IDE. My guess lies on a bug in the gather program. Unfortunatly I don't have gather's source code because it's part of natively programs of the controller.