Unable to set up Intel Edison on Windows
I fixed it by following these steps (through trial and error, I don't really understand what I did but it works ...)

I am using Windows 8.1, 64 bit edition.


Download the Edison firmware from https://software.intel.com/en-us/iot/hardware/edison/downloads. For me it was http://downloadmirror.intel.com/25028/eng/edison-image-ww25.5-15.zip.
Extract the zip file.
Start the Windows Command Prompt as Administrator.
The extracted archive should contain a file called "flashall.bat". Change to the directory containing the file.
Connect all micro-USB ports and the barrel connector. At this point Windows did not recognize the Edison as a flash disk. This is part of what I was fixing.
Follow the steps in my question until the output on the console (also from my question) appears.
Run "flashall --recovery"
Run "flashall". When "Please plug and reboot the board" appears, disconnect the A (or middle) USB port and the barrel connector for the power. At this point everything is switched off. Then reconnect A and the barrel connector to reboot the board.
Wait about 5 minutes for the rest of the process to run automatically.


At this point everything should work again.

You should see this on the command line in Windows:


C:\Users\_\Desktop\edison-image-ww25.5-15>flashall --recovery
Starting Recovery mode
Please plug and reboot the board
Flashing IFWI
!!! You should install xfstk tools, please visit http://xfstk.sourceforge.net/

C:\Users\_\Desktop\edison-image-ww25.5-15>flashall
Using U-boot target: edison-blankrndis
Now waiting for dfu device 8087:0a99
Please plug and reboot the board
Dfu device found
Flashing IFWI
Download        [=========================] 100%      4194304 bytes
Download done.
Download        [=========================] 100%      4194304 bytes
Download done.
Flashing U-Boot
Download        [=========================] 100%       237568 bytes
Download done.
Flashing U-Boot Environment
Download        [=========================] 100%        65536 bytes
Download done.
Flashing U-Boot Environment Backup
Download        [=========================] 100%        65536 bytes
Download done.
Rebooting to apply partiton changes
Dfu device found
Flashing boot partition (kernel)
Download        [=========================] 100%      6111232 bytes
Download done.
Flashing rootfs, (it can take up to 5 minutes... Please be patient)
Download        [=========================] 100%    566330368 bytes
Download done.
Rebooting
U-boot & Kernel System Flash Success...
Your board needs to reboot to complete the flashing procedure, please do not unplug it for 2 minutes.

C:\Users\_\Desktop\edison-image-ww25.5-15>