Twitterrific makes a request for all previous replies and direct messages from Twitter. This can include replies and direct messages from quite awhile ago depending on how often you receive them.
Also, since neither Twitterrific or Twitter keep track of whether they are read or not, they will show up as unread tweets. You can easily mark them as read using the “catch up” keyboard shortcut: Command-K.
In a future release, we plan on tracking read and unread state across launches.
We've tried to anticipate most questions you might have. However, if you can't find the answer you're looking for here, send us your query and we'll answer it personally.