Yesterday I received my first Galileo and followed the instructions to download the latest IDE to my system, power up the board, plug in the USB and wait for the device driver install to fail. Note: it showed up differently then the instructions on this machine. Trying to remember, it either showed up like a Teensy like device or it may have been like an Atmel USB device... Should have written it down. But I went and updated the driver and it then properly showed up in the device manager as Galileo (COM65). So I loaded up the IDE, selected COM65, tried to update Firmware, and after do I have power question, it failed to retrieve the current version. I played around for awhile with no luck. Note: I plugged in the debug terminal cable and saw that it was booting properly, and used the SD card method, to see if the board was working.
So I went to my notebook computer and installed the IDE, plugged in the board and followed the instructions, it showed up as Galileo (COM6), started up the IDE, tried to do the firmware update and it worked. Also was able to download the blink program. I checked out the Comm device in the device manager and it is using the same version of: c:\windows\system32\drivers\usbser.sys
So went back to my main machine tried downloading blink on this machine and it still failed. So, I went into the Device Manager and changed the Galileo Comm port to COM6 tried again and sure enough, the IDE could retrieve the firmware version and it also can also download blink
So my guess is some of your tools can not handle Com ports >64. I did not test to see where the breaking point is. Could be 64, 63, 32...