It seems that the problem is not related to the certificate. The "Unknown Certificate warning." refers to server certificate, not the client one.
In Rebex log we can see that the TLS was successfully established, so the server certificate was validated and accepted.
Please, check 4 things:
1. you are connecting to the same server (same IP address).
In Rebex log, line: Connecting to none proxy at *******:990.
In FileZilla log, line: Connecting to ***.***.***.***:990...
2. you are using the same username
3. you are using the same password
4. username and password contains only ASCII characters (non-ASCII characters can be encoded differently)
Please, let us know the result.