I didn't take any timings on Studio 4, but my impression is that Studio 6 is much slower in downloading code than AVR32 Studio 4 was. (Or maybe it is because the progress bar does not updating...) My application size is 114310 bytes, AT32UC3B0256 part. When I click the start debugging button, the time from the click to the application start is using JTAGICE mkII 1 min 25 sec, and I need to click a timeout window once. using a Dragon, the time is slower as expected, but not as much as expected, 1 min 45 sec.
Maybe my system has a problem? Atmel says that JTAGICE mkII "Uploads 256Kb code in ~30 seconds", while on Dragon it should take twice as long. I certainly don't get anywhere close to these. Do you see similar timings? Is there a setting somewhere I could try? The "Atmel Communication Timeout" setting does not seem to affect anything.
The firmware image on my JTAGICE is 7.19, which the Studio says is up to date.
But I'm still not going back to Studio4, the 6 is finally almost where it should be (and the interrupts can be skipped in debugging, thank you very much for this!).