Issues with programming Diecimila

I am having some issues programming one of the sample sketches on the board. I think I may have screwed something up while trying to setup AVRStudio and the USBICE mkII.
When running the Arduino 0017 software, I load the Blink sample code. It verifies fine but when I try to program the board I get the following errror:

avrdude: stk500_getsync(): not in sync: resp=0x00
avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x51

I have my boad connected to my pc through USB, but I have a USB to Serial converter on the board. I have COM5 selected and I have the correct board selected. There should be a bootloader on the board.
Any help would be appreciated.

Edit: I just grabbed a second board and hooked it up and everything programmed fine. So, I think I may have screwed something up when trying to use the JTAGICE mkII. I think it has something to do with the debug wire or spi setting.
I have read a bunch of the posts on here that suggest it may be a com port issue or a bootloader issue. The com port settings are fine becasue I was able to upload to another board.
The board in question worked when I first connected it to my JTAGICE mkII because it was able to read the device signature.
I don't think I did anything to blow out the bootloader, when I try to read the device signature now, I get an error with the communication method and it tells me its using ISP. So, everything should be good.

Somebody? A little hint?

I have read a bunch of the posts on here that suggest it may be a com port issue or a bootloader issue. The com port settings are fine becasue I was able to upload to another board.

So it's the boot loader. Don't know how you did it but that's what is wrong.

Thank you for the reply.
If it was a bootloader problem, shouldn't I still be able to read the device signature or hardware registers? I can't see any registers or do any accesses with the JTAGICE mkII.