This problem only occurs when running the Java Firmware upgrade tool from my Linux environment.
Upgrading the board firmware from a MacOS environment worked strangely - maybe it is the Java version on my Linux machine.
On my Mac, I have:
$ java -version
java version "1.7.0_67"
Java(TM) SE Runtime Environment (build 1.7.0_67-b01)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
Anyway, I discovered a nice command to copy files between the HOST and Galieo board:
$ lsz --escape --binary --overwrite firmware-1.0.4.cap < /dev/cu.usbmodem1421 > /dev/cu.usbmodem1421
Only, what are .cap files? And how must these get executed to do the actual SPI flash firmware upgrade?
Have you tried using this method? Intel® Galileo - Programming SPI Flash through the UEFI Internal Shell
The .cap file along with the .efi file are needed to perform this process and successfully update the firmware.
Let me know if this works