Yes, we had a similar discussion about the bootloader somewhere in this forum (or maybe another forum?).. The 1200bps trigger won't erase the flash.. it just simply send the sam chip to the bootloader... The bootloader makes the soft erase and programs your sketch..
Hard erasing and reseting the chip will send it to the bootloader (ROM, as you found in the datasheet.. No, this is not the problem that's preventing us from communicating with SAM-BA..
May I ask why you need to use sam-ba?