I have this same issue. If I do not boot off SD card, the COM port appears and works fine to upload sketches.
As soon as I boot from SD card, the COM port does not appear in Device Manager.
I loaded LINUX_IMAGE_FOR_SD_Intel_Galileo_v1.0.0.7z onto the SD card.
I updated Galileo firmware to 1.02.
I confirmed that it was booting from SD card by connecting to FTDI serial output using putty. Python is available and I select mass storage in the boot menu.
Ejecting the SD card and rebooting to Galileo flash image fixes the issue every time.