We use two DKP pools and had trouble getting automatic adjustments working correctly. It seemed as if it would always pull the value from the default/main pool and use that for the secondary pool.
Looking into the code for apa_decay_current.class.php I noticed what looked like potentially problematic use of dkp_id in get_value(). Sometimes it uses $dkp_id and sometimes it uses $data['dkp_id']. It looks like most callsites for this function would pass in array() for $data, which may make it use the wrong DKP pool for certain calculations.