As explained in our article dedicated to Joomla Plugin ordering, the order of plugins in your Joomla site is important.

Plugins are executed in the order they have in the Plugin Manager (under menu 'Extension' in the Joomla! administrator side).

Email Protector cloaks the email addresses that it finds at the stage it triggers. Normally, you will not run into any issues.

However, if you're using 3rd party plugins to output your content, such as Articles Anywhere - and any of those articles contain email addresses you want to cloak, then you need to make sure that Email Protector is ordered after Articles Anywhere, otherwise, Email Protector will be triggered before Articles Anywhere outputs the content.