Hello 
Im really confused what to do now. I've sitted 2 days trying to start sanguino bootloader on ATmega644PA, and first i got an error when trying to flash it , but it was problem with line in makefile : LDSECTION = --section-start=.text=0x1F000(that 1 is causing this ), when i deleted that 1 finally bootloader has flashed to MCU, but there is problem when i tried to send blink example. It always give error :avrdude:
Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.
Tried all possible versions of Arduino IDE nwewer and older same error . Anyone know what to do ? What i need to change to get it working?
Which bootloader are you trying to use? (and which sanguino distribution, for that matter.)
I'm inclined to believe that the standard sanguino bootloader (from http://code.google.com/p/sanguino/downloads/detail?name=Sanguino-0101r1.zip ) should be linked with .text starting at 0xF800 (it's a 2kbyte bootloader), which makes that whole bootloader directory pretty suspect. OTOH, it'll depend on what the fuses have been set to.)
The Sanguino-0023r2.zip file has section-start at FC00, which also looks wrong.
Sanguino-0018r2_1_4.zip has section-start at F800; maybe you should try that bootloader.
(note that the bootloader can change or not change, entirely independently of the core libraries and IDE version.)
Im using that version Sanguino-0101r1, i set LDSECTION = --section-start=.text=0x1F000 in makefile. And here is my question what fusebits i need to set and how the boards.txt should be for that Atmega644p. I've tried multiple settings for that board.txt and nothing, same error with wrong device signature. As far as i know nobody has solution for this problem. I've read somewhere that bootloader Sanguino-0018r2_1_4 should work but same problem with signature . So i don't know really how to properly set makefile and fuses to get this working.
Ok , i give up . None of the bootloader works. I tried all of them and same invalid signature error.
What signature is it showing? (turn on verbose uploading in the preferences dialog.)
When trying to upload sketch its says : Device signature = 0x000000
In boards.txt i have :
##############################################################
atmega644p.name=Sanguino W/ ATmega644P / 644PA
atmega644p.upload.protocol=stk500
atmega644p.upload.maximum_size=63488
atmega644p.upload.speed=38400
atmega644p.bootloader.low_fuses=0xFF
atmega644p.bootloader.high_fuses=0xDC
atmega644p.bootloader.extended_fuses=0xFD
atmega644p.bootloader.path=atmega644p
atmega644p.bootloader.file=ATmegaBOOT_644P.hex
atmega644p.bootloader.unlock_bits=0x3F
atmega644p.bootloader.lock_bits=0x0F
atmega644p.build.mcu=atmega644p
atmega644p.build.f_cpu=16000000L
atmega644p.build.core=arduino
Fuses are same as in boards.txt
.............................................
Ok finally i solved my problem 
Boards.txt
##############################################################
atmega644p.name=Sanguino W/ ATmega644P / 644PA
atmega644p.upload.protocol=arduino
atmega644p.upload.maximum_size=63488
atmega644p.upload.speed=38400
atmega644p.bootloader.low_fuses=0xFF
atmega644p.bootloader.high_fuses=0xDC
atmega644p.bootloader.extended_fuses=0xFD
atmega644p.bootloader.path=atmega644p
atmega644p.bootloader.file=ATmegaBOOT_644P.hex
atmega644p.bootloader.unlock_bits=0x3F
atmega644p.bootloader.lock_bits=0x0F
atmega644p.build.mcu=atmega644p
atmega644p.build.f_cpu=16000000L
atmega644p.build.core=arduino
##############################################################
Fuses set as above and i make a new bootloader.hex with 0xF800 bootloader sector.I got Ftdi chip to make TX/RX to the board and DTR is not resetting MCU properly so i need to manually reset it when sending a sketch .
When trying to upload sketch its says : Device signature = 0x000000
In boards.txt i have :atmega644p.name=Sanguino W/ ATmega644P / 644PA
atmega644p.upload.protocol=stk500
Ah hah. Change that line to: atmega644p.upload.protocol=arduino
See Google Code Archive - Long-term storage for Google Code Project Hosting.
(different bootloader, but could be the same problem.)