I see - I need to have a read of all that code today.
So... the 1200 bps part isn't actually a specification of the SAM chip itself - but, a sketch uploaded by the Arduino IDE that is now on the chip, detects the opening and closing of the USB port at 1200bps, and triggers and erase and pulls the SAM-BA bootloader out of ROM ready to be used.
I didn't realise the SAM could be reset, erased and prepared from software - I thought it was a hardware thing, or a 'hard-wired' sequenced such as 1200bps open and close from the factory.
I'll try this this evening, but my guess is then - if I upload some code from Atmel Studio using ASF code and BOSSAC, and then try and program the board using the Arduino IDE - i'll probably have to press the erase and reset button myself?
Page 327 (331 specifically) of the full SAM3X8E datasheet has the details of entering the programming mode...
Just a thought baselsw - regarding our issues with SAM-BA. When one erases the SAM chip with the erase button, and hit's reset, I don't think this actually pulls the SAM-BA out of ROM ready to be used by SAM-BA, I think it just erases the flash ready to be written to by something like BOSSAC. Actually, erasing the chip and resetting it must use the SAM-BA software out of the ROM, as it deals with serial communications.
The datasheet is a little unclear on all of this - what do you think?
EDIT - Here we go, straight from the datasheet -
"Setting GPNVM Bit 1 selects the boot from the Flash, clearing it selects the boot from the ROM.
Asserting ERASE clears GPNVM Bit 1 and thus selects the boot from the ROM by default."
So, erasing the chip boots the chip from ROM, where SAM-BA is contained. So I guess the way the programming port works, it clears the GPNVM bit, and resets the chip - so that it boots from ROM, and then uses BOSSAC to erase the flash prior to uploading new code.
So no, that dosen't explain our issues with the SAM-BA GUI...