Excellent, glad you got things going.
Nice mod with the cable too. I think it's a wise precaution to disconnect the 3.3v from the USB interface, otherwise the 4.5v from the AAs will be fed back up it.
The USB-BUB that JC supplies, and the TTL-R232-5V cable I use (from moderndevice), supply 5 volts to the PWR line on the FTDI connector, from here the VR produces the 3.3v the RFM12B and ATmega require. So having the onboard VR is very useful. You were unlucky in that you already had a 3.3v supply from your USB interface (I must admit I have never seen one of these).
I think the reason it was designed like this is that 99% of the people with previous ATmega experience are coming to the JeeNode from 5v boards, and therefore have 5v FTDI cables.
You could go one step further with your USB mod, find the 5v line on the mini-USB connection and connect that to your blue wire. Then you wouldn't required the battery when you were developing. The power connections are on the pins at each end. One side will be ground, the other 5v from the PC USB.