Loading bootloader on ATMega2560

I'm working on a prototype of a board using a ATMEGA2580 and trying to use these instructions and code to load the bootloader:

http://www.emartee.com/Modules/bbs/viewthread.php?tid=742&extra=page%3D1

I use the Arduino "Burn Bootloader" and after a couple of minutes I get the error that others have reported using USBTinyISP on the Arduino Mega:

avrdude: verification error, first mismatch at byte 0x3e000 0x0d != 0xff avrdude: verification error; content mismatch

I assume the the bootloader is getting loaded, but when I plug into the onboard USB I do not get a port setup in Windows. I'm guessing the problem is in the RT232RL circuits. I used the same layout for a previous prototype with an ATMega1280 and it worked fine.

The PB7 (D13) led is flashing about every 5 seconds so the CPU seems to be alive. Can anyone confirm that if only the bootloader is loaded that the D13 LED flashes?

I'm using a USBTinyISP clone but I've ordered a genuine AVR programmer to try and I'm going to review the USB circuits and check for shorts, etc. If all that fails I may pull the 2560 and replace it with a 1280.

I would try and make sure the fuse bits are being set correctly. Maybe use avrdude from the command line to see what the fuse bits are.

The genuine AVRISP mkII programmer fixed the problem and the prototype works fine now.