We just ran in to this problem, yesterday (March 19). Our Web Dev team brought a new customer, and no matter what they did, they could not connect to our Enhance APP servers (we tried a couple) with ftp and SSL.
I have also had this problem about a week before we upgraded from 11.04 to 12.29....
In this case, that customer was more than willing to move to FTP over SSH, so problem solved...
Two tickets in short order makes me think that ftp.<domain>.<tld> is not being included in the LE query... am I missing something?