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First, ensure the keypair is correct and associated to the Instance. If correct, you can follow the steps on the documentation Connect to your Linux instance from Windows using PuTTY to connect to the Instance.
Note if the .ppk keypair is not working, retry creating a .pem key then Convert your private key using PuTTYgen to connect to the Instance
If the issue persists. Feel free to Contact AWS Premium Support
I briefly tested connecting to an AMI2 EC2 machine via Ubuntu on my laptop. I encountered a number of problems trying to connect with SSH. One was solved by ensuring the ssh key had rw or read only permission to the owher only (rw------- or r-------- permissions). I think it's an SSH v3 feature. The users home directory should also be tied down to the user only.
I'm not sure about AWS Ubuntu instances, but also make sure you connect to your cloud machine using the correct username.
Best of luck
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