Comments and sidebar Problem

To whom it may concern,

I am not sure what started the problem, but I will give all information that its possible to help me to find the possible failure.

First problem: Suspiciously the right sidebar can be visualized only in the index page,when before it could be seen in every blog´s page.

Second problem: The comments module doesn´t charge in the entries page, and don´t allow the users leave comments or even read them.

First possible cause: Recently my blog has been a victim of a hacker, because of that I had to restore some older archives of previous versions, the involved directories were “home” and “wp-includes”, obviously when I accesed to the WP-admin it notified me that I had a previous version and pending updates, so I updated again.

Second possible cause: As security measure, I have changed the “root” user from the database for another one with the same privileges and configured it in the “wp-config.php” file. Does WordPress vinculates any information with the user that connects to the database?

Sincerely I don´t have the knowledge, could you help me to solve the failure? What archives would be involved? It must be wrong replace them with older backups?

Version: WordPress 2.9.2
URL: http://www.rammstein.com.uy
Theme: Pyrmont V2 2.0.6

Thank you in advance,