Problem using the FTDI cable with the Arduino Pro

Most Arduino boards came with RS232 or USB. My Arduino Pro came without. I tried to use the FTDI cable with my board and the Arduino IDE. I can only load the sketch the first time. After the first time, the IDE would not recognize the board. I had to reload the bootloader to work. I did some research and found out the FTDI cable use RTS# for the reset pin and normal Arduino uses DTR# pin for reset. Then I got a FTDI Basic Breakout from Sparkfun which uses the DTR# for reset and it works fine.
Does anybody have this problem and share some light on this? I want to able to use the FTDI cable, what is need to modify the IDE to use either RTS# or DTR# to reset the board before downloading the sketch?

If it doesn't have DTR, the auto-reset won't work, you'll need to manually reset the board as you upload the sketch. I find if I click on the upload button, wait until it reports the sketch size and then press and release the reset quickly it works.

Update:

I found a post on "Arduino Forum ? Hardware ? Troubleshooting ? Arduino FTDI upload works only once, then locks up" and I set the the RTS on close flag in the 'advanced' COM port settings for the COM port corresponding to the FTDI cable. I can upload my sketches every time now.