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You can take a look at Star Explorer. It allows you to download a gallery, a whole category or your whole site. You can specify what to do if there's already a local copy. So you could set it to skip any photos that you already previously downloaded. Here's a screenshot of the download dialog. Captions and keywords are also included in the photos ...

What you describe sounds indeed like the result of the automatic rotation being applied. If your camera comes with a orientation sensor, it'll still save portrait photos in the same landscape orientation and just attach the EXIF orientation tag to include what orientation the photo was taken in. Upon uploading, SmugMug automatically rotates photos lossless ...