SSH with key passphrase not working
PuTTY is using different key format than the OpenSSH and OpenSSH is failing to report correctly the errors about unknown format in some versions.

If you want to use the PuTTY key in OpenSSH, you need to convert the private key to OpenSSH format in PuTTYGen (as described on SO):


Open PuttyGen
Click Load
Load your private key
Go to Conversions->Export OpenSSH and export your private key
Copy your private key to ~/.ssh/id_rsa