Thanks to http://codeigniter.com/forums/viewthread/73804/#366081 and some bits of information from some CI folk that I follow on twitter (I asked em): Eric Barnes, Dan Horrigan, Phil Sturgeon and Zack Kitzmiller, I found a solution. If you are a CodeIgniter n00b like me, you may like to follow these guys.
I deleted init.php and config.php, then jammed the following into the bottom of my CI's config.php (I am also autoloading from a custom library called mylibrary).
function multi_auto_require($class) {
if(stripos($class, 'CI') === FALSE && stripos($class, 'PEAR') === FALSE) {
foreach (array('flourish', 'mylibrary') as $folder){
if (is_file(APPPATH."../auxengines/{$folder}/{$class}.php")){
include_once APPPATH."../auxengines/{$folder}/{$class}.php";
}
}
}
}
spl_autoload_register('multi_auto_require');
Works brilliantly. Thanks, people!