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Hi "hkiehs",
We have the same problem with the EVAL-KIT and on mass production of our products based on AT91SAM9G45, the problem is on the UTMI PLL at power up. So you can start up the PLL again using the reset button after the power up (turn on) and the board will be recognized by the PC host. So, be careful about the jumper setting to disable the NAND Flash chip select and start the SAM-BA monitor.
We have produced 1000 boards with this MCU and we got aprox. 20% of this failure, some MCUs has the issue.
To fix the problem on normal operation is more complex, you will need to modify the ATBootstrap code.
The solution from Atmel for this issue reported on Engineering Samples Errata is to use the serial DBGU interface or a Dataflash to run a modified ROM boot. You can find a n explanation of the issue on the MCU datasheet too.
For more info write to this FAQ.
Best regards,
RL
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