I just tried upload via the Native port on Ubuntu Linux 14.04 and IDE 1.6.6. No trouble here.
Sketch uses 10,092 bytes (1%) of program storage space. Maximum is 524,288 bytes.
Forcing reset using 1200bps open/close on port /dev/ttyACM0
PORTS {/dev/ttyACM0, /dev/ttyS0, } / {/dev/ttyS0, } => {}
PORTS {/dev/ttyS0, } / {/dev/ttyS0, } => {}
PORTS {/dev/ttyS0, } / {/dev/ttyACM0, /dev/ttyS0, } => {/dev/ttyACM0, }
Found upload port: /dev/ttyACM0
/home/me/.arduino15/packages/arduino/tools/bossac/1.6.1-arduino/bossac -i -d --port=ttyACM0 -U true -e -w -v -b /tmp/build100cd442213b82cc4265ca32481a5c7e.tmp/Blink.ino.bin -R
Set binary mode
readWord(addr=0)=0x20001000
readWord(addr=0xe000ed00)=0x412fc230
readWord(addr=0x400e0740)=0
readWord(addr=0x400e0940)=0x285e0a60
version()=v1.1 Dec 15 2010 19:25:04
chipId=0x285e0a60
Connected at 921600 baud
readWord(addr=0)=0x20001000
readWord(addr=0xe000ed00)=0x412fc230
readWord(addr=0x400e0740)=0
readWord(addr=0x400e0940)=0x285e0a60
Atmel SMART device 0x285e0a60 found
write(addr=0x20001000,size=0x34)
writeWord(addr=0x20001030,value=0x40)
writeWord(addr=0x20001020,value=0x20010000)
writeWord(addr=0x400e0a00,value=0x600)
writeWord(addr=0x400e0c00,value=0x600)
Device : ATSAM3X8
readWord(addr=0)=0x20001000
readWord(addr=0xe000ed00)=0x412fc230
readWord(addr=0x400e0740)=0
readWord(addr=0x400e0940)=0x285e0a60
Chip ID : 285e0a60
version()=v1.1 Dec 15 2010 19:25:04
Version : v1.1 Dec 15 2010 19:25:04
Address : 524288
Pages : 2048
Page Size : 256 bytes
Total Size : 512KB
Planes : 2
Lock Regions : 32
Locked : readWord(addr=0x400e0a08)=0x1
readWord(addr=0x400e0c08)=0x1
writeWord(addr=0x400e0a04,value=0x5a00000a)
readWord(addr=0x400e0a08)=0x1
readWord(addr=0x400e0c08)=0x1
readWord(addr=0x400e0a0c)=0
readWord(addr=0x400e0a08)=0x1
readWord(addr=0x400e0c08)=0x1
writeWord(addr=0x400e0a04,value=0x5a00000a)
readWord(addr=0x400e0a08)=0x1
readWord(addr=0x400e0c08)=0x1
readWord(addr=0x400e0a0c)=0
readWord(addr=0x400e0a08)=0x1
readWord(addr=0x400e0c08)=0x1
writeWord(addr=0x400e0a04,value=0x5a00000a)