Special sections in the .elf file start above 0x810000 and must be removed when generating a hex file for programming a particular memory, e.g.
$ avr-objdump -h webserver6.avr-atmega128rfa1
webserver6.avr-atmega128rfa1: file format elf32-avr
Sections:
Idx Name Size VMA LMA File off Algn
0 .data 00001bda 00800200 0000e938 0000ea2c 2**0
CONTENTS, ALLOC, LOAD, DATA
1 .text 0000e938 00000000 00000000 000000f4 2**1
CONTENTS, ALLOC, LOAD, READONLY, CODE
2 .bss 000031a6 00801dda 00801dda 00010606 2**0
ALLOC
3 .eeprom 00000029 00810000 00810000 00010606 2**0
CONTENTS, ALLOC, LOAD, DATA
4 .fuse 00000003 00820000 00820000 0001062f 2**0
CONTENTS, ALLOC, LOAD, DATA
5 .signature 00000003 00840000 00840000 00010632 2**0
CONTENTS, ALLOC, LOAD, READONLY, DATA
So,
avr-objcopy -O ihex -R .eeprom -R .fuse -R signature ipso.elf ipso.hex
alternately, only copy the desired sections:
avr-objcopy -O ihex -j .text -j .data ipso.elf ipso.hex