I got my netduino in the mail and whatever was flashed on it was toast, so after a few posts on the forum I got great advice on how to flash the Boot Loader (TinyBooter) and firmware (ER_CONFIG and ER_FLASH)
Erase the chip by applying +5v to the gold pad located by pin 12
Run the SAM-BA application from ATMEL (Note if your on windows 7 Ultimate stick with an older version of SAM-BA, do not use 2.10.)
The current package I have installed is from: Install_AT91-ISP_v1.13.exe
Power up the netdruino by connecting the power and serial TX/RX on pin 1 & 2 (Note: make sure you have completely removed power after sending +5v to the gold pad)
Chose serial port and board
If the first time does not succeed power down and try again. And if it still does not succeed try hitting the gold pad for a second time.
If SAM-BA can communicate and get a valid id on the chip you should be presented with the following screen
Choose a file to send while in the “Flash” tab.
Click Send File. The SAM-BA application isn’t that great and locks up while sending data over the serial port. If possible just wait. This part of the process will take a while, even if you don’t see data being sent over the serial port stuff is going on.
SAM-BA will ask you if you want to “lock involved lock region(s) (0 to 2)”, I choose “No” on this.
At this point you should have succeefully flashed the Boot Loader onto the netduino mini. Click on “Compare sent file with memory” to ensure the Boot Loader did not get corrupted in the process. If everything is fine you should be presented with something similar to the following screen.
While still in the “Flash” tab execute the script “Boot from Flash (GPNVM2)” by clicking on the “Execute” button. The terminal on the bottom of the app should display “-I- GPNVM2 set”