xbee not communicating with x ctu when connected through arduino

My Xbee gets connected to the system, if connected through the shield available for connecting Xbee's directly to the system and XCTU is able to communicate with the modem and I could configure it. But, when I connect the same Xbee through Arduino + Wireless SD Shield + Xbee, the XCTU software is not able to communicate with the modem.. What could be the reason?

Do you have code running on the arduino when you connecting?

Yes, I did.. A code was running in the Arduino when I attempted to connect the Xbee to the system

If you want to communicate with Xbee module using arduino.Arduino will act just as a USB to Serial.So you can not run any code on it. just a empty code.
void setup() { }
void loop() { }

You need to change the jumpers from USB to Xbee if you are not using the USB port to change parameters on the xbee.