SSH Cygwin Password not recognised

I have recently been using Cygwin to coect 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 coect via the Cygwin console. I've been given root access and I coect via 'ssh [email protected]'. Each time I try to coect it says 'permission denied' and after 3 incorrect attempts it states 'Permission denied (publickey,password).'. I know the password is correct as when I coect via SFTP on WinSCP, after I generated a .ppk private key in authentication I can coect 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 coected 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?