I'm getting this PHP warning in my error_log and want to get it fixed. I'm told it is loaded within php.ini which I've verified as well as a bunch of configuration settings for the module. I'd like to maintain the module configuration in the place where it's loaded so I need to find out how else to remove it from the list.
Unless removing it from php.ini is just fine.
Module 'eAccelerator' already loaded
It sounds to me like you've got the configuration in multiple files.
If your set up is on Debian (or something like Debian) it could be that eAccelerator is loaded in php.ini as well as in a secondary file. For instance, on Debian, php.ini lives at /etc/php5/apache2/php.ini (for PHP 5.x and Apache 2.x). But it also parses all the files in /etc/php5/conf.d/, which in my case includes files like gd.ini, mysql.ini, and suhosin.ini. I have see misconfigured packages add configuration to the end of php.ini as well as in a separate file in conf.d. This will give the kind of error you're seeing.
FYI, this scanning is done with a compile-time configure option (specifically, --with-config-file-scan-dir=).