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While looking at the JeeNode v3 electric diagram I thinks there's a mistake about the connection of capacitor C1, no? It is connected between FTDI pin 6 and ATMEGA pin 1 before the pullup resistor R1. Shouldn't the C1 be connected to ground instead of directly to FTDI pin 6?
Also in the picture 'JN3 pinout.png' file you named the FTDI pin as RTS, sujesting the serial interface ReadyToSend... it should be RST...
This is providing an auto-reset feature used by Arduino and friends.
Check out the "DTR through .1 uF cap" sketch at this link:
http://dorkbotpdx.org/blog/feurig/usingthedorkboardwithotherpeoplesprogrammers
I believe either DTR or RTS can be associated with FTDI pin 6.
Ok, my mistake... after looking at your link I guess this is Arduino stuff and a way of reseting to program the micro-controller... I'm not familiar with Arduino...