onQueueComplete wasn't firing and I think I found the problem. I'm not familiar with javascript or Uploadify, so I could just be doing something wrong.

function onUploadComplete(file) {
var stats = swfuploadify.getStats();
swfuploadify.queue.queueLength = stats.files_queued;
if (swfuploadify.queue.uploadQueue[0] == '*') {
if (swfuploadify.queue.queueLength > 0) {
swfuploadify.startUpload();
} else {
swfuploadify.queue.uploadQueue = [];
if (swfuploadify.settings.onQueueComplete) swfuploadify.settings.onQueueComplete(stats);
}
} else {
if (swfuploadify.queue.uploadQueue.length (Should be: swfuploadify.queue.queueLength ?) > 0) {
swfuploadify.startUpload(swfuploadify.queue.uploadQueue.shift());
} else {
swfuploadify.queue.uploadQueue = [];
if (swfuploadify.settings.onQueueComplete) swfuploadify.settings.onQueueComplete(stats);
}
}