I know this is an old thread, but it helped me and I wanted to offer the workaround devised with the information here: With some trial and error we found that creating a .ssh folder in the cygwin root (c:\Tools\cygwin64 in this case) and copying the necessary known_hosts and id_rsa files from the user's home (c:\Tools\cygwin64\home\tsstester\.ssh in this case) to the new location (and removed all non-user access via cygwin chmod, unsure if absolutely necessary) resolves the issue.
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