My guess is a problem with libusb, I was not able to get avrdude to work with my libusb based ISP tools when I had Atmel Studio installed, and I suspect other USB drivers can cause problems as well. I don't have these problems on Linux, all the ISP tools I have worked fine there. I guess it is just that I can not put Atmel Studio on Linux.
I use the ArduinoISP sketch (that is in examples) for most things now. I load it into an Uno and then use that as the ISP tool. It works when both Atmel Studio and Arduino IDE are installed. At this time I am doing most of my work with the AVR toolchain from Linux, and the Uno with the ArduinoISP sketch is still my goto ISP tool.