I've a WordPress 2.1.3 installation on which I've Akismet 2.0 spam block plugin installed. The problem I've had is that even when Akismet was deactivated, it was still silently blocking comments. As a deactivated plugin the blocked comments were not visible in the admin user interface.
I noticed the problem when multiple of my blog readers started to complain that they cannot get comment trough to my posts. I activated Akismet again and noticed that it had been working and blocking these comments even when deactivated. As far as I understand the WordPress behaviour, no plugin should get executed when it's deactivated. Have I understood this correctly? If so there is either a bug in WordPress 2.1.3, my installation has got somehow corrupted or my Glued Ideas theme is somehow intervening the WordPress default behaviour.