Can not log to ec2 instance with ppk nor pem key pair files using Putty or Filezilla

I have a Ubuntu 16.04.2 LTS EC2 instance running on AWS and I can logon with

ssh -i "file.pem" ubuntu@ec2....sa-east-1-compute-amazonaws.com

But I haven't been able to log in with filezilla (ubuntu 22.04) or Putty (windows 10) for years now. All I get is the "Server refused our key" message and also there's nothing related on /var/log/auth.log, even after editing the /etc/ssh/sshd_config file on line:

Subsystem sftp /usr/lib/openssh/sftp-server -l INFO

I've tried every combination of RSA key-pair there is available on Puttygen and even made a new ed25519 key-pair on AWS Console, then added it to ~/.ssh/authorized_keys and successfully tested it with the same ssh command. Also, the listed private keys on the autorized_keys file seems to be the same, but with only 1 line (the generated keys have line breaks).

So what am I missing? I've read something on how after a client release update some keys become outdated, but haven't been able to overcome this.

I'm using the latest Putty (0.79) and Filezilla (3.58.0).

Any help would be greatly appreciated!