hmm... i was under the impression that the auto-reset signal was done by configuring the FTDI driver to do so automatically, not by the Arduino IDE
see Boarduino - Breadboard-compatible Arduino Clone
where it reads:
If you'd like to have the auto-reset capability, make sure C6 is soldered in. With Mac's and Linux it should just work fine.
If you're using Windows you'll need to make a slight change to the driver preferences. In the Device Manager, select the USB COM port
Then right click and select Properties
Click on the Port Settings tab, and click on Advanced...
Make sure Set RTS On Close is selected.
Personally, I find auto-reset useless when I used Arduino, but I've long since stopped using Arduino since I got my programmer.