When trying to use a SFTP RSA passcode, in version 4.6 pressing the Login button results in nothing happening (and a beep in Yosemite like there was a problem). In 4.6.1 the passcode won't even prompt and an authentication error is returned.
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Would it be possible for you to create a new key pair that does not work and attach it here.
I'm not sure what you mean by a new key pair? When I log in, I submit my username and password, then get a RSA time based passcode request based on my pin for two-factor auth. Are you requesting a time period / passcode pair?