I did install freshly Arduino IDE 1.6.4 on an old 32bit Linux Thinkpad T42.
All went well, including installing Due support via Boards Manager.
Compilation of sketch went fine, but upload did not succeed with error message "bossac: extra arguments found". This thread was very helpful in solving the Due platform.txt bug:
This simple diff for platform.txt did resolve the issue, uploading works fine now:
$ diff .arduino15/packages/arduino/hardware/sam/1.6.8/platform.txt.orig .arduino15/packages/arduino/hardware/sam/1.6.8/platform.txt
106c106
< tools.bossac.upload.pattern="{path}/{cmd}" {upload.verbose} --port={serial.port.file} -U {upload.native_usb} -e -w {upload.verify} -b "{build.path}/{build.project_name}.bin" -R
---
> tools.bossac.upload.pattern="{path}/{cmd}" {upload.verbose} --port={serial.port.file} -U {upload.native_usb} -e -w {upload.params.verify} -b "{build.path}/{build.project_name}.bin" -R
$
Since I did not get hits for this issue here on Forum search (only bossac.exe issues for Windows) it seems nobody does program Due with Arduino IDE from32bit Linux -- but its works.
Hermann.