Have you imported your public and private key into FlashFXP? Specifically the private key as the public key is used by the server to verify the authentication.
After importing the key into FlashFXP you then select it for use by the site profile, this is done from within the Site manager > select the site > Connection tab, click the Apply button to save the changes.
Assuming you've done the following it should work, if it doesn't I would be more than happy to test compatibility with serv-u if you can provide me with a test account on the server. You can send this information to me via a
private message.
If you generated the key pair within FlashFXP make sure that the public key is in a format recognized by serv-u and is properly set in serv-u.