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When the SSH tools are used by Git executable, it will use the value in the HOME environment variable which contains the path to the SSH settings to be used by Git. You can set an environment variable by right-clicking My Computer/Computer in your start-menu then selecting Properties. Click the Advanced system settings heading and you should see this dialog:
Click Environment Variables.
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Make sure you are logged in as the same user the Continua server is run under. Click the New button in the section for User variables.
Enter HOME for the Variable name and %USERPROFILE% for the Variable value.
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If you're prompted for a password, then something went wrong with the private/public key setup.