Are you running these commands in the void setup or the void loop part of your program? What happens if you run those commands directly? Do you mind posting your Arduino sketch?
It was in the setup function, but never mind, I've solved the problem.
The system calls doesn't work well, sometimes they do, sometimes part of it, etc, but using the sh script it does work perfectly.
To send the server to the background I added the character "&" at the end of the command.
The script would be like this:
rdate 220.127.116.11 && hwclock --systohc
node /media/mmcb1k0p1/Server/server2.js &