For the record: the USB problem was resolved by switching to gcc 4.8.
This one works (from the Arduino IDE 1.6.5's Due package):
gcc version 4.8.3 20140228 (release) [ARM/embedded-4_8-branch revision 208322]
... while this one fails (installed from https://launchpad.net/gcc-arm-embedded):
gcc version 4.9.3 20150529 (release) [ARM/embedded-4_9-branch revision 227977]
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For the record: the USB problem was resolved by switching to gcc 4.8.
This one works (from the Arduino IDE 1.6.5's Due package):
gcc version 4.8.3 20140228 (release) [ARM/embedded-4_8-branch revision 208322]
... while this one fails (installed from https://launchpad.net/gcc-arm-embedded):
gcc version 4.9.3 20150529 (release) [ARM/embedded-4_9-branch revision 227977]