Make sure that your magento cron is running every minute. We are using a cronjob to process the notifications. The cronjob will be executed every minute. It only executes the notifications that have been received at least 2 minutes ago. We have built in this 2 minutes so we are sure Magento has created the order and all save after events are executed. A handy tool to get insight into your cronjobs is AOE scheduler. You can download this tool through Magento Connect or GitHub
