SSH key directory defaulting to non-Cygwin SSH client location

[J J <1301mail@gmail.com>]

I recently had to reinstall cygwin on my Windows 7 laptop and am now
having trouble getting passwordless ssh to work from my laptop to
remote hosts. I have another ssh client, Reflections, installed, and
Cygwin insists on using that directory for the ssh key. I would like
to use a separate .ssh directory but can't figure out how to work
around this behavior.

Here's my home directory that the shell opens to. This is also in
/etc/passwd of course:
/home/jd2013 pwd
/home/jd2013

Here's what happens when I try to generate an RSA key file:
/home/jd2013 ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter name for key file: jd2013
C:\Users\jd2013\Documents\Attachmate\Reflection\.ssh\jd2013 already exists.
Overwrite (y/n)? n

I don't know for certain how this was working before I had to
reinstall Cygwin (McAfee had a false positive that bash.exe was a
virus last month), but I would like to avoid having to set my Cygwin
home to the Reflection directory. I tried creating a .ssh subdirectory
in $HOME, but that had no effect. For what it's worth, $HOME is owned
by "jd2013:Domain Users" and the Reflections directory is owned by
"Administrators:Domain Users".

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