I'd read somewhere about the capacitor on the arduino
reset line connecting it to the USB RTS/CTS line
causing problems. This isn't the original article
I read, but it talks about the same problem:

http://husks.wordpress.com/2010/02/21/modify-an-arduino-for-debugwire/

Apparently, that capacitor can cause problems with
the AVRDragon board debugging your arduino,
and the author shows how to remove the cap.




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