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UPDATED!

It is now considered best practice to simply edit the nsswitch.conf file located under DRIVE:\cygwin64\etc\ and add the line:

db_home:    windows

Also, be sure to add "C:\cygwin64\bin" to your PATH Environment Variables.

I use cygwin openssh to allow me to ssh to *Nix machines.  One problem after initial install is that cygwin cannot save the ssl cert on your PC because the default path is wrong.  Here is how to fix that.

Find the "passwd" file usually located here "C:\cygwin64\etc" on a default 64bit install.  Edit the file in notepad and change the following line.

FROM: /home/username

TO: /cygdrive/c/users/username

where "username" is your windows login.  Please note that "cygdrive" in the above path is the actual text you need to use.  This is not the path for cygwin.

Save the file and you are good to go.