I suggest doing what WildBill suggested and communicate with the box using Hyperterminal first to confirm the controller is working as expected.
We have tested the control box/stepper motor setup using labview directly from the PC, and it works. We have not used HyperTerminal to check it, but perhaps that will help.
If you used a null-modem cable to talk to the computer, you need a straight-through cable to talk to the controller, and vice versa. Or you need to change the Arduino end from DTE to DCE or vice versa.
I am a little confused. We are trying to run the setup without the use of a computer.. we have only been running the signal through the TTL to RS232 converter to the PC to test if we could convert the serial communication to an RS232 feed (ie convert 0-5V signal to +/-3-12V signal). Are you saying I need to change the Arduino end from DTE to DCE to communicate with the control box regardless? That could be the problem..