When defining Discussion Boards in Site Definition (in ONET.XML), the subjects of discussion threads point to default.aspx. This means that when clicking on a discussion subject the user is redirected back to the same page. Subject links should point to flat.aspx.
Some blogs (1, 2) mention a KB article related to this problem and also a MS hotfix that might fix this problem, but it doesn't.
Add ContentTypeID="0x012001" into the View element of the Discussion web part in your site definition like this:
ContentTypeID is now allowed there according to the schema, but it will still fix the issue.