This is a bug introduced by the AVR 1.6.12 boards that came with the 1.6.10 IDE.
Upgrading the AVR boards will trigger it elsewhere too. They updated the avrdude version and then released without testing burn bootloader (or much else - which unfortunately is par for the course here)
1.6.9 with AVR boards 1.6.11 is fine - that's what I recommend people use currently.