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I have recently been using Cygwin to connect to an Ubuntu box which I host my server on, however it has just been reset completely. Previously I had no issues using Cygwin however I recently re-made my SSH key and reinstalled Cygwin.

My issue now is that once I gave my SSH pub key to the box administrator, I can no longer connect via the Cygwin console. I've been given root access and I connect via 'ssh [email protected]'. Each time I try to connect it says 'permission denied' and after 3 incorrect attempts it states 'Permission denied (publickey,password).'. I know the password is correct as when I connect via SFTP on WinSCP, after I generated a .ppk private key in authentication I can connect perfectly fine with the password.

Please help, I've been trying to fix this for the past 2 days. >.<

P.S I'm not crazy good with SSH and Cygwin so bare in mind I may not have the answer to all of your questions, but if you give me commands as such I may be able to find out the answers for you.

EDIT: I used Gitbash instead of Cygwin and it connected perfectly fine, therefore it must be an issue with Cygwin.. as much as my issue has been partially resolved, does anyone have any ideas on what may be causing this?

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  • Even if the issue is with the Cygwin executable (or libraries that it depends on), using the server to help troubleshoot may be informative. Check the authentication log ( ls -lt /var/log | head then less /var/log/auth.log or whatever file your operating system uses). Presumably it may say something different, which may provide a clue. I'm presuming you're using OpenSSH-p under Cygwin; if so, try: ssh -i privkey [email protected]
    – TOOGAM
    Commented May 13, 2016 at 20:44

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If Cygwin fails password validation for Ubuntu

vi /home/<youraccount>/.ssh/known_hosts

and delete the rows (specially for the IP address of the Ubuntu), save, and try to login after a minute.

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