1. It is a little confusing, now you mention it. The difference is that the big check box on the left marks a task a done, and the other (small) checkbox is used to select a bunch of tasks so you can do bulk actions. At this point there is only bulk-complete, but adding tags by bulk is something you want to relatively often, so that's why we can't really get rid of the second check box. On the other hand, it is weird to have two check boxes for every todo, so we'll have to think of something.
2. Correct, D is discuss. The D button can be toggled so other people can see the todo should be discussed first. Suppose I want to work on a feature, and Wim realizes that it won't work because of X, he can click the 'D' button and add a comment. When I then go to my task list I see the 'D', I check the comments and realize what's wrong. We found that a simple flag that says "hey - wait a second" is a really effective way to indicate a possible problem.
3. Very annoying. We wanted to fix it, but we couldn't justify waiting any longer with the beta.
1. It's confusing to see the equivalent of two checkboxes on the left, one that is an icon and one that is an HTML checkbox. What is the difference?
2. In general, the icons could be a little more intuitive. I'm not sure what "D" means (discuss maybe? Then why is a discuss button also on the left?
3. Going to a new page to discuss / comment is kind of annoying. I'd prefer something like FriendFeed-style inline commenting.
Good luck and thanks for the invite!