As Joakim Lubeck wrote:

> I found that it works if I do an explicit flash erase before writing
> the flash with avrispmkii/XMega128a1. I did not have to do that with
> the JTAGICE3.

Hmm, I switched Xmegas to use page erase (rather than chip erase) by
default when reprogramming application flash.  Perhaps there's still a
bug in that ...
-- 
cheers, Joerg               .-.-.   --... ...--   -.. .  DL8DTL

http://www.sax.de/~joerg/
Never trust an operating system you don't have sources for. ;-)

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