Which version you are using? It is recommended always use latest version.
You can use hooks to change almost anything of this plugin, so that you will not lose any changes when you update this plugin.

To change checkbox output you can add following code in your theme’s functions.php

add_action( 'fep_message_table_column_content_fep-cb', function(){
    if ( fep_current_user_can( 'send_new_message' ) ) {
        ?><input type="checkbox" class="fep-cb" name="fep-message-cb[]" value="<?php echo fep_get_the_id(); ?>" /><?php
    }
});