I have just come out of a serious problem when trying to program a recently acquired XMega32A4 chip.
Here's the deal. When I tried programming the chip with avr dragon, I succeeded on the first try. When I tried programming it a second time, it failed. It erases and programs it fine, but on the verification it fails. Fuses are read fine as well, some can be programmed and some fail at verification. On the peculiar note, I could debug it fine (AVR STudio 5), to me it was very strange!
After tinkering and reading lots of posts in search of a solution. I came about a very important tip, "programming speed". It made me think about how ISP and JTAG have speed limitations upon programming depending on the chips oscillator, being it internal or external.
So, with that in mind, I went to the AVR Studio 5 programming window, the one titled 'AVR Programming', and searched through the fuses. My interest went to one fuse called SUT. SUT or StartUp time probably has to do with speed, so i changed it to 0. Probably fastest, correct me if I am wrong.
After I did that, I have not had any troubles with programming the Xmega32A4.
Anyways, that's all. I just wanted to share the experience if someone is using the AVR DRagon and had trouble. Apparently using the MKII works right out of the box, and dragon doesnt after the initial programming.
IMHO, Atmel could change the default speed of the avr dragon to slow it down or something in reflection of the selected SUT setting.
Have a nice day.
EDIT: This was my solution to the problem I had. Most likely no the only problem out there. So, some feedback would be nice for future reader's orientation.