I have upgraded the plugin to version 3.01 today, running on WordPress 3.3.1, and after doing that, my [email] shortcodes stopped working. I just see the opening and closing shortcodes surrounding the email addresses.
It is a know thing. The plugin is coded to clear all previous entries. This is because, the plugin was coded from bottom and the old data was not good to migrate into new one.
Now the data is stored in a perfect way. So future versions wont have any problem.