Since the last update (?) I had a problem with my FTP-SSL connection: connecting would take ages, and finally the directory would be shown as empty. The same connection would work under FTP, though.

I tried your "common problems" suggestions disabling STAT, LIST, MLSD commands in all possible combinations - nada. As Filezilla would connect OK, I knew it was not my server's problem, but comparing the log files wouldn't get me any closer to a solution - they were more or less identical.

I took me some time, but I found the culprit: in Cyberduck's preferences on the FTP tab, I disabled "try to encrypt data channel using TLS". An unlikely place to look at, but all was well.