I just installed Word Stats on two blogs, and found that while stats on the edit page were correct, on the dashboard page some posts were being shown with 0 words. This is both on the diagnostics for too-short posts, and the totals. Keywords from these posts were also missing, as I confirmed by selecting a time period containing only one post.
Based on one of the other threads here, I checked a few of the problem posts for nbsp entities and found them. Replacing the entities with spaces fixed the problem.
This was with WordPress 3.5 and Word Stats 4.3.1.