When I want to run GUI programs on the drabonboard I simply use
ssh -X to get the X11 ports forwarded:
ssh -X linaro-alip
I usually use a GNU/Linux desktop but this approach should also work with a Cygwin rootless X server (or similar). Basically if you have things setup correctly to run
xclock from a cygwin bash shell (i.e. run
xclock on your Windows machine) then you should have everything configured correctly for X11 port forwarding.