Arduino-0011 comes with avr-gcc that already supports atmega644. :-?
You can validate it by running
%ARDUINO_HOME%\hardware\tools\avr\bin\avr-gcc --target-help
Look for "Known MCU names:" section. It contains every AVR module this compiler build supports.
Here is mine produced by stock arduino-0011 avr-gcc.
Known MCU names:
avr1 avr2 avr3 avr4 avr5 avr6 at90s1200 attiny10 attiny11 attiny12
attiny15 attiny28 at90s2313 at90s2323 at90s2333 at90s2343 attiny22
attiny26 at90s4433 at90s4414 at90s4434 at90s8515 at90s8535 at90c8534
at86rf401 attiny13 attiny2313 attiny261 attiny461 attiny861 attiny24
attiny44 attiny84 attiny25 attiny45 attiny85 atmega603 atmega103
at43usb320 at43usb355 at76c711 atmega48 atmega8 atmega83 atmega85
atmega88 atmega8515 atmega8535 atmega8hva at90pwm1 at90pwm2 at90pwm3
atmega16 atmega161 atmega162 atmega163 atmega164p atmega165 atmega165p
atmega168 atmega169 atmega169p atmega32 atmega323 atmega324p atmega325
atmega325p atmega329 atmega329p atmega3250 atmega3250p atmega3290
atmega3290p atmega406 atmega64 atmega640 atmega644 atmega644p atmega128
atmega1280 atmega1281 atmega645 atmega649 atmega6450 atmega6490
atmega16hva at90can32 at90can64 at90can128 at90usb82 at90usb162
at90usb646 at90usb647 at90usb1286 at90usb1287 at94k atmega2560
atmega2561
Do you have any other avr-gcc installed (though I doubt it will cause a problem)? It's been a while since I looked at arduino IDE source but if I remeber correctly it keeps looking for avr-gcc within it's own %ARDUINO_HOME% directory structure.
Could this be a problem with line endings in your boards.txt file after copy/paste? This is just a guess. :-/
Can you post atmega644 portion of your boards.txt file?