Flash programming fails

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I had some problems with breakpoints not doing what they should, and code seemingly resetting after breakpoint continuation. I don't know how breakpoints work here, but in ancient times it was by replacing instructions. So I tried to just program the code into the chip to see if this might be the cause. And after programming verify failed. It seems I can erase the chip, but programming will successfully program just a K or two.

I have more than one of my PCBs prepared, and using another works fine (so far).

Is there anything I could have done wrong that makes the possible number of flash cycles really low? I did turn breakpoints on/off and make program changes. But hey, how many can I do in less than a week?

I'm not stuck. But if I'm doing something wrong killing my processors, I would like to change my ways. I'm not a typical killer person.

From .HEX to be programmed:
:100280000810021000000000000000000000000044
.. and continuing with lots more hex data..

What it reads back:
:1002800008100210000000000000FFFFFFFFFFFF4A
.. and then FF from there on.

What I use:
ATXMEGA128A3U-AU. Target voltage 3.35V.

JTAGICE MkII Sn:070000003497. Used for debug & program.

Atmel AVR Studio 5 (Version: 5.0.1038.1038)
© 2011 Atmel Corp.
All rights reserved.

OS Version: Microsoft Windows NT 6.1.7600.0
Platform: Win32NT

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Einar Sjaavik