Flashing Marlin Firmware to Atmega2560 verification error; content mismatch

Hello, We have designed our own Atmega2560 printed circuit board and trying to flash Marlin in it. I am using avrdudess 2.13 which uses avrdude version 6.3.

>>>: avrdude -u -c usbtiny -P usb -b 115200 -p m8 
Detected 1e9801 = ATmega2560
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
>>>: avrdude -u -c usbtiny -p m2560 -P usb -b 115200 -e -U flash:w:"C:\Users\caner\Downloads\Marlin.ino.with_bootloader.mega (1).hex":a 

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: erasing chip
avrdude.exe: reading input file "C:\Users\caner\Downloads\Marlin.ino.with_bootloader.mega (1).hex"
avrdude.exe: input file C:\Users\caner\Downloads\Marlin.ino.with_bootloader.mega (1).hex auto detected as Intel Hex
avrdude.exe: writing flash (261406 bytes):

Writing | ################################################## | 100% 100.82s

avrdude.exe: 261406 bytes of flash written
avrdude.exe: verifying flash memory against C:\Users\caner\Downloads\Marlin.ino.with_bootloader.mega (1).hex:
avrdude.exe: load data flash data from input file C:\Users\caner\Downloads\Marlin.ino.with_bootloader.mega (1).hex:
avrdude.exe: input file C:\Users\caner\Downloads\Marlin.ino.with_bootloader.mega (1).hex auto detected as Intel Hex
avrdude.exe: input file C:\Users\caner\Downloads\Marlin.ino.with_bootloader.mega (1).hex contains 261406 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 64.67s

avrdude.exe: verifying ...
avrdude.exe: verification error, first mismatch at byte 0x0000
             0xff != 0x0c
avrdude.exe: verification error; content mismatch

avrdude.exe done.  Thank you.

We are getting this when we try to flash marlin firmware hex.
However, when I try blink.hex output is

Blink.ino.with_bootloader.standard.hex: 1,250 / 262,144 Bytes (0.48%)
>>>: avrdude -u -c usbtiny -P usb -b 115200 -p m8 
Detected 1e9801 = ATmega2560
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
>>>: avrdude -u -c usbtiny -p m2560 -P usb -b 115200 -e -U flash:w:"C:\Users\caner\Documents\Blink\Blink.ino.with_bootloader.standard.hex":a 

avrdude.exe: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude.exe: Device signature = 0x1e9801 (probably m2560)
avrdude.exe: erasing chip
avrdude.exe: reading input file "C:\Users\caner\Documents\Blink\Blink.ino.with_bootloader.standard.hex"
avrdude.exe: input file C:\Users\caner\Documents\Blink\Blink.ino.with_bootloader.standard.hex auto detected as Intel Hex
avrdude.exe: writing flash (32768 bytes):

Writing | ################################################## | 100% 1.13s

avrdude.exe: 32768 bytes of flash written
avrdude.exe: verifying flash memory against C:\Users\caner\Documents\Blink\Blink.ino.with_bootloader.standard.hex:
avrdude.exe: load data flash data from input file C:\Users\caner\Documents\Blink\Blink.ino.with_bootloader.standard.hex:
avrdude.exe: input file C:\Users\caner\Documents\Blink\Blink.ino.with_bootloader.standard.hex auto detected as Intel Hex
avrdude.exe: input file C:\Users\caner\Documents\Blink\Blink.ino.with_bootloader.standard.hex contains 32768 bytes
avrdude.exe: reading on-chip flash data:

Reading | ################################################## | 100% 0.72s

avrdude.exe: verifying ...
avrdude.exe: 32768 bytes of flash verified

avrdude.exe done.  Thank you.

Not having problem trying to flash blink.hex so is there anyone who has an idea where should I look to find the error hero?
BTW The .ino file that we extract the marlin.hex is working fine for the arduino mega no problem to compile it.

Waiting for your helps. Thank you for your interest.

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