I would suggest you to download the latest Arduino IDE software (1.6.5), I believe you’ll get better results using the new IDE, https://www.arduino.cc/en/Main/Software. Unlike the Arduino IDE 1.6.0, where the packages for the Galileo and Edison boards are already there, in the Arduino IDE 1.6.5 you’ll probably need to download the packages manually, from the Board Manager menu, under the Tools tab.
Open the Arduino IDE > Click on Tool > Go to Board: (a different board should be already selected by default, e.g: Yun) > Boards Manager > Search the Galileo package and download it.
Regarding the issue with the board firmware, try with the Intel Galileo Firmware Update Tool, this should solve the issue.
Again on my learning curve about Intel Galileo gen2. My config
** Win7 64 bits (portable PC)
** Arduino IDE 1.6.5
** INTEL Galileo gen2 board
** Board Firmware 1.0.4 installed
** Jack powered by 8V (2S LiIon 18650)
I tried "blink L 13" from Arduino IDE (via USB client)
a) Compiling successful
b) Upload transfer complete
c) Blink 13 is running well (L Led is blinking)
Now my new question-problem
When I power the Galileo Gen 2 again (after a no power status) the L Led is not blinking
I suppose the program Blink L13 is not launched
Is it necessary to burn a boatloader on my Galileo ?
This usually happens when you use the SPI-Flash image of your Galileo. I would suggest you download the uClibc or eglibc image from the Downloads page, IoT - Intel® Galileo Board Download | Intel® Developer Zone. Just put the image into as SD card and insert it to your Galileo. By default, your board should boot from there. That way you shouldn’t have any problem uploading sketches and running them even after rebooting the board.
You can check the differences between both images in this thread Re: what the difference between the 2 Linux Images?.
Finally I have downloaded the official Galileo Image on my microSD
And all is OK
The Arduino IDE sketch "blink LED pin 13" is now launched after around 1 minute (after power ON)
On the root I have (for your info) one subdirectory "boot" and four files
boot\grub\grub.conf (1 ko)
bzimage (1938 ko no extension)
core-image-minimal-initramfs-cpio.gz (1653 ko)
grub.efi (274 ko)
image-full-galileo-clanton.ext3 (307200 ko)
I suppose the file grub.efi is the launcher
PS I have a 2S LiIOn 18650 pack on the jack ... Great