As soon as you turn on the auto-uploader it finds and uploads your replays. It will also do this automatically after finishing games, so you don't have to click / upload. It's possible that you just uploaded more files than you realized since the auto-uploader found all of them, and you manually uploaded some.
If there's more games on the site than in the replay log it's possible that other users are uploading replays that you are playing in, that you did not upload.
Posted: Jan 27, 2015