Hi TMacie,
It sounds like some plugin is causing the action/filters to be called twice. Try doing this:
1. Add the following filter to your functions.php:
add_filters( 'bbpnns-dry-run', '__return_true' );
This will keep it from actually sending out the emails to all your members.
2. Add the error_log( __LINE__ );
lines to the plugin to see what is getting hit. It should be showing one set of line numbers in the logs, not 2. The messages are written to the webserver’s error logs by default. You can change that by setting a couple more parameters. e.g., to get a log file under the same directory as the plugin, use this:
error_log( __LINE__, 3, dirname( __FILE__ ) . '/log.txt');
3. Reactivate each plugin one by one, saving a topic or reply (in the topic/reply editor screen) while the ‘Notify’ checkbox is ticked. That will force the plugin to populate the logs.
Let me know what you find.