Could you advise please - in FTP Profiles - on the Authentication tab - you have the ability to enter a Private key file - however this appears to be global - rather than related to a specific FTP site - as all the other tabs are - how does one use BC3 with multiple sites - each requiring a different private key file?
Beyond Compare 3 does not support per FTP site private keys. This is something we would like to work on for a future version of BC3. I've added your note to our wishlist entry on the subject.
Aaron P Scooter Software