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I also just finished making a board using the AT91SAM3S1B using a 12MHz Crystal. SAM-BA recognizes the chip over USB and I am unable to send a bin file larger than about 12kB otherwise it hangs. I am able to perform the "Boot from Flash (GPNVM1)", unplug the USB, plug it back in and see that the chip no longer shows up under the USB list. If I set the ERASE jumper on my board, which pulls the ERASE pin high, then unplug the USB and plug it back in then the device shows back up on the USB list and SAM-BA can once again communicate with the chip. Unfortunately all of my test programs are larger than 12kB, so I cannot test my blinking LED code yet. Is there an updated version of SAM-BA or a work around by modifying the TCL scripts? Please let me know if I can provide any more information to help resolve this problem.
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