Agreed. If I remember correctly it even destroyed a site once when it was attempting to make sure their validator could reach the verification file. I just did what everyone said: "it's so easy, just run it on auto mode with apache and it'll configure your cert for you". Turned out to be a huge PITA.
Recently I had to renew that site again (I've been postponing and dreading it) and looked for a different client. The getssl bash script[1] had its own problems (all caused by me not taking the time to read the readme, but the default settings were a bit odd), but overall a 10× better experience than the official client. Much less magic, much more a unix-like tool ("it does only one thing, and one thing very well").