Gen7 v1.3.1 Atmega644 Electronics Bootloader Upload

I have a Gen7 v1.3.1 board that I am trying to get working for the first time.

I am having trouble uploading the bootloader. I am using a Polulu USB AVR Programmer (http://www.pololu.com/product/1300) and Windows 8. I am following the instructions here (http://reprap.org/wiki/Gen7_Arduino_IDE_Support#Bootloader_Upload). I have tried this on two different Atmega644 chips and get the same error.

Setting the fuses seems to work fine, but uploading the firmware gives the error.

avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x0000
         0xff != 0x00
avrdude: verification error; content mismatch

Let me know if there is any other information I can give that would be helpful. Thanks.

The following is the last part of the command line output when I try to upload the bootloader.

Reading | ##############################################     | 92% 1174.93savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | ###############################################    | 93% 1184.94savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | ###############################################    | 94% 1199.97savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | ################################################   | 95% 1210.02savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | ################################################   | 96% 1225.06savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | #################################################  | 97% 1235.08savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | #################################################  | 98% 1250.11savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | ################################################## | 99% 1265.18savrdu
de: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
Reading | ################################################## | 100% 1275.24s

avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x0000
         0xff != 0x00
avrdude: verification error; content mismatch

avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_cmd(): short reply, len = 0
avrdude: safemode: lfuse changed! Was f7, and is now 2
Would you like this fuse to be changed back? [y/n] n
avrdude: safemode: hfuse changed! Was dc, and is now 2
Would you like this fuse to be changed back? [y/n] n
avrdude: safemode: efuse changed! Was fc, and is now 2
Would you like this fuse to be changed back? [y/n] n
avrdude: safemode: Fuses OK

avrdude done.  Thank you.