There is a new installer called Intel® Galileo Firmware Updater Tool in http://www.intel.com/support/galileo/sb/CS-035101.htm . I’d suggest you to download the one that suits your OS and try to upload once again. In https://downloadcenter.intel.com/download/24748 you’ll find the firmware updater user guide for instructions on how to update. Try this and let me know your results.
Ok, the issue is resolved. My Galileo Gen2 was a loaner system and I was given a 5V power supply. When I upgraded the firmware to 1.0.4 I started seeing the issue mentioned in my first post. Now I got a 12V power supply and I don't see that issue. Strange thing is I did not see the issue when it was on the 1.0.2 firmware.
Thanks for your help Sergio. btw, I did download the latest Intel firmware updater as well and it showed firmware version as 1.0.4.