I think I already know the answer, but I want to check.
For the ISP header on the AVR dragon I have pin 1 connected to PDI_DATA, Pin 2 connected to my target voltage which is 3.3V, Pin 5 connected PDI_CLK, and Pin 6 connected to the target ground.
The Dragon reads that the target is 3.3V, but is unable to read the Device ID. I noticed by accidentthat I had the CLK and the DATA lines backwards before. Are the PDI lines sensitive enough to cause damage if they are wired backwards or do I have some other problem?