Custom ATMEGA 2560 board

I have a custom ATMEGA 2560 board that is displaying odd behavior. I am using a Pocket Programmer to interface with the board. The ATMEGA is running at 3.3V 8MHz. I am able to program the ATMEGA with a sketch through the Arduino IDE, but I am unable to get a bootloader to correctly upload. I am trying to burn the bootloader from Sparkfun's Mega Pro 3.3V (Mega Pro 3.3V - DEV-10744 - SparkFun Electronics). The boads.txt file is below. Does this point to a bootloader compatibility problem?

###################################################################
mega2560v.name=Mega Pro 2560V 3.3V

mega2560v.upload.protocol=stk500v2
mega2560v.upload.maximum_size=258048
mega2560v.upload.speed=57600

mega2560v.bootloader.low_fuses=0xE2
mega2560v.bootloader.high_fuses=0xD4
mega2560v.bootloader.extended_fuses=0xFD
mega2560v.bootloader.path=
mega2560v.bootloader.file=MegaPro3.3V-8MHz-57600.hex
mega2560v.bootloader.lock_bits=0xCF

mega2560v.build.mcu=atmega2560
mega2560v.build.f_cpu=8000000L
mega2560v.build.core=arduino:arduino
mega2560v.build.variant=mega
###################################################################

The ATMEGA [2560] is running at 3.3V 8MHz.

That is more than likely your problem.

You need an Atmega2560V to run at that voltage:

– ATmega2560V/ATmega2561V:

• 0 - 2 MHz @ 1.8V - 5.5V, 0 - 8 MHz @ 2.7V - 5.5V

Normal (non V) chip needs higher voltage:

– ATmega2560/ATmega2561:
• 0 - 16 MHz @ 4.5V - 5.5V