OK, so if I understood it right it works with AVRStudio at least to the point that you can connect to the controller. But it does not work with Arduino 1.0 / AVRDude because it does not find the programmer. This is most likely a driver issues. However since I am working with Linux I can not verify any hints on this.
This may or may not be a solution.
http://www.avrfreaks.net/index.php?name=PNphpBB2&file=viewtopic&p=468532