This is still not working, and it is very frustrating.
I have uploaded to 1.0.0 (SPI) and rebuilt an eglibc version of the image-full-galileo target to fix opencv.
The above problem remains ... however it is only a problem when using the Arduino IDE from a Linux host.
From a Windows host, communication over serial/zmodem between the IDE and the Galileo work fine.
The problem is that you have to use the rebuilt cross-compiler toolchain to make sketches for eglibc ...and I only know how to rebuild the cross compiler toolchain for Linux. It would be massively hacky to make the Windows IDE download sketches built by the Linus toolchain.
I have spent many hours experimenting with this and the fact that the Arduino IDE for Linux just won't talk to the Galileo properly at all strikes me as very odd: surely I am not the first person to try to build Arduino sketches for eglibc Linux and try to download them from Linux??