Problem with Arduino Fio Wireless programming

Hi everybody

I have an arduino fio board and experiencing a lot of difficulties with the wireless programming through xbee.
First, I tried to upload a sketck to arduino fio board through FTDI cable and I was able to do so.But the problem rise when I try to program the board wirelessly through the xbee modules.
I am doing the exact same thing that the website is suggesting. I use 2 Xbee s1 modules and a sparkfun XBee Explorer USB adapter (which I modified and put a jumper between DIO3 and RTS). The xbees are talking together, (I have tested them on two xbee to serial adapter) but when I put one of the xbees on fio board, I am not able to upload sketches through that.
I am using a usb cable to power the fio board. I do configure the two xbee radios with fio xbee config tool. one of them as the programming radio and the other as the fio radio. But When I try to upload the sketck via xbees, the following error shows up:

avrdude: stk500_getsync(): not in sync: resp=0x32

Can some one please help me figure out what the problem is?
I am uploading the same sketch as the one i uploaded through wire. should I change it? (I mean should I specify some where that i am going to use xbee?)
I have to say that while I am trying to upload the sketch wirelessly, the RSSI LED on both explore kit and fio is lit and also the TX led blinks also the D13 led blinks as well.

could you guys please help me figure out what is the problem?

I am doing the exact same thing that the website is suggesting.

What web site?

The Arduino website for Arduino fio programming.