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Hi, this problem seems to be in the avrdude.conf.in file. I replaced
avrdude.conf.in file from avrdude 5.6 with the file from avrdude 5.8,
compile 5.6 and voila, I got the error

I attached the part from ATxmega128A1 from 5.6 and 5.8 and a screenshot
from diffuse, comparing both files.

http://roboter-gallery.de/pub/avrdude/diff.png

Hope this helps.

Markus
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#------------------------------------------------------------
# ATxmega128A1
#------------------------------------------------------------

part
    id               = "x128a1";
    desc             = "ATXMEGA128A1";
    signature        = 0x1E 0x97 0x4C;
    has_jtag         = yes;
    has_pdi          = yes;
    nvm_base         = 0x01C0;

    memory "eeprom"
        page_size       = 32;
        size            = 2048;
      ;

    memory "flash"
        size            = 0x20000;
        page_size       = 512;
      ;

    memory "boot"
        size            = 0x2000;
        page_size       = 512;
      ;

# signature is actually in IO address space
    memory "signature"
        size            = 3;
        offset          = 0x90;
      ;

    memory "fuse0"
        size            = 1;
        offset          = 0x20;
      ;

    memory "fuse1"
        size            = 1;
        offset          = 0x21;
      ;

    memory "fuse2"
        size            = 1;
        offset          = 0x22;
      ;

    memory "fuse4"
        size            = 1;
        offset          = 0x24;
      ;

    memory "fuse5"
        size            = 1;
        offset          = 0x25;
      ;

    memory "lockbits"
        size            = 1;
        offset          = 0x27;
      ;

    memory "calibration"
        size            = 512;
      ;

    memory "usersig"
        size            = 512;
        offset          = 0x200;
      ;

  ;
#------------------------------------------------------------
# ATXMEGA128A1
#------------------------------------------------------------

part
    id          = "x128a1";
    desc        = "ATXMEGA128A1";
    signature   = 0x1e 0x97 0x4c;
    has_jtag    = yes;
    has_pdi     = yes;
    nvm_base    = 0x01c0;

    memory "eeprom"
        size            = 0x0800;
        offset          = 0x08c0000;
        page_size       = 0x100;
        readsize        = 0x100;
    ;

    memory "application"
        size            = 0x00020000;
        offset          = 0x0800000;
        page_size       = 0x100;
        readsize        = 0x100;
    ;

    memory "apptable"
        size            = 0x00002000;
        offset          = 0x0081e000;
        page_size       = 0x100;
        readsize        = 0x100;
    ;

    memory "boot"
        size            = 0x00002000;
        offset          = 0x00820000;
        page_size       = 0x100;
        readsize        = 0x100;
    ;

    memory "flash"
        size            = 0x00022000;
        offset          = 0x0800000;
        page_size       = 0x100;
        readsize        = 0x100;
    ;

    memory "prodsig"
        size            = 0x200;
        offset          = 0x8e0200;
        page_size       = 0x100;
        readsize        = 0x100;
    ;

    memory "usersig"
        size            = 0x200;
        offset          = 0x8e0400;
        page_size       = 0x100;
        readsize        = 0x100;
    ;

    memory "signature"
        size            = 3;
        offset          = 0x1000090;
    ;

    memory "fuse0"
        size            = 1;
        offset          = 0x8f0020;
    ;

    memory "fuse1"
        size            = 1;
        offset          = 0x8f0021;
    ;

    memory "fuse2"
        size            = 1;
        offset          = 0x8f0022;
    ;

    memory "fuse4"
        size            = 1;
        offset          = 0x8f0024;
    ;

    memory "fuse5"
        size            = 1;
        offset          = 0x8f0025;
    ;

    memory "lock"
        size            = 1;
        offset          = 0x8f0027;
    ;
;
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