I assume you're autofocusing the lens? My experience with using the focus adjustment on a Canon 35/1.4 is similar. Using AF, sometimes the lens is brutally sharp, sometimes it's a little off. I suspect it's just the nature of AF, there's a little bit of slop at each point in the system that usually cancels itself out, but sometimes is cumulative and leads to unsharp photos.
If I have to shoot at f/1.4 I tend to refocus a LOT and shoot a lot of photos. (By refocus I mean defocus the lens manually then hit the thumb button again to focus. Single Shot focus is more reliable, as is the center point focus on a 5D2.)