Does Mollom track user reputations?

Yes, Mollom uses identity information (like Drupal's user id of the posting user) when it is available, and "remembers" past activity. Posting spam can damage a user's reputation, while posting legitimate content with a low spam score enhances it. The reputation of a user is part of Mollom's algorithm for evaluating posts, so posts by a user with a reputation of "spam" is more likely to be flagged for a CAPTCHA challenge. Because Mollom weights recent user activity higher than past activity, internal reputations decay over time; this means that no one is ever permanently flagged by Mollom's filter.