[Marco van Herwaarden]

Are they in the list showing as read after you have read them?

What Read Marking type do you use? Cookie or database based?

Try Updating your thread counters in AdminCP -> Maintenance -> Update Counters

Also to further troubleshoot this, please remove any hacks and disable your plugins, then see if you still have this problem.

Note: To temporarily disable the plugin system, edit config.php and add this line right under <?php

define('DISABLE_HOOKS', true);

If so, reupload all the original vB non-image files (except install.php). Make sure you upload these in ASCII format and overwrite the ones on the server.