I just installed context 3 on my drupal 6 site. I updated ctools to latest version (1.9) as suggested. Everything looks fine and I can enter conditions and reactions. The problem is that nothing happens. I see no reaction at all on the behavior of my site. Any hits to where I should start looking for the source of the problem?
Start with a sanity check - make sure your rules "make sense" and that you set them up correctly. Try to apply the same context rules on a clean install.
If it works there and not in your existing site (with content, other modules and customized configuration), clone that site and try disabling modules one by one to see where the conflict is. It's hardly possible to say where the problem is without knowing any details about your existing installation.