I'm not sure if this will help anyone debug this but I tried to use the AVR ISP programmer within the Arduino IDE and received the following:
C:\arduino1\hardware/tools/avr/bin/avrdude -CC:\arduino1\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega2560 -cstk500v2 -P\.\COM5 -b115200 -D -Uflash:w:C:\WINDOWS\TEMP\build5740842602492432075.tmp\BlinkTest.cpp.hex:i
avrdude: Version 5.11, compiled on Sep 2 2011 at 19:38:36
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is "C:\arduino1\hardware/tools/avr/etc/avrdude.conf"
Using Port : \.\COM5
Using Programmer : stk500v2
Overriding Baud Rate : 115200
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: ser_send(): write error: sorry no info avail