When it comes to tracking productivity in UX design, the focus should always be on the outcomes, quality and hitting key milestones, and not on day-to-day activity. Because there is no one "perfect" UX design process (just as there is no one perfect software development process) each project is going to have different timeliness and needs. One project may be heavy on detailed design documentation, and is easier to "track" than one that is focused on user research and foundational understanding.
But even with a project that is "documentation-heavy", you have to be careful not to fall into the "to do list trap" of just crossing off things. Here's why: You can get all your design work done in a timely matter, but if the design sucks, who benefits? Certainly not the user, and definitely not your company. Yes, you will "look good" in the short term, in that management sees you are "hitting your dates"… but you will be burned later if the design was rushed and ill-concieved. Trust me, I've been there.
How does an individual designer measure his own productivity? There are many different techniques I have seen and used, including the GTD methodology. But in the end, I think UX design isn't about "productivity" it's more about problem solving, and making a difference for users. So I look at satisfaction as a more important personal metric around my design work than the number of UI widgets I can crank out in a week.
As a design manager, how to track productivity? Well, in addition to the above, I make sure that the designers have time to refine, iterate, and fail. Yes, fail. We learn a lot by piloting early designs with users and finding out what doesn't work. Identify key milestones, let the designers follow the process that they are comfortable with, and focus on quality. Keeping in mind, of course, that deadlines are absolutely necessary as a motivator and a way to "focus the brain."