Hmm yes I remember I got that problem as well and here is my correction -
The fix seems to be change AS6 to be the sames as the arduino-1.5.1r2 in
C:\Program Files\Atmel\Atmel Studio 6.0\extensions\Atmel\ARMGCC\3.3.1.128\ARMSupportFiles\Device\ATMEL\sam.h
/* Entire SAM3XA series */
#define SAM3XA_SERIES (SAM3X4 || SAM3X8 || SAM3A4 || SAM3A8)
from
#define SAM3XA_SERIES (SAM3A4 || SAM3A8)
I got it from
\My Documents\Arduino\arduino-1.5.1r2\hardware\arduino\sam\system\CMSIS\Device\ATMEL\sam.h
/* Entire SAM3XA series */
#define SAM3XA_SERIES ( SAM3X4 || SAM3X8 || SAM3A4 || SAM3A8)
Let me know if that works for you.
Background: The fix is in the AS6 toolchain so it makes me nervous.
I did send it through to Eric Weddington Jan 10th,2013 and though he responded, he didn't say if the fix I proposed was good.
I see from
that there is another release
Atmel Studio 6.1 beta (build 2440)
and 6.1 has an upgraded ARM Toolchain 4.7.2
from AS 6.0 ARM Toolchain 4.7.0.59 - GCC 4.7.0