EXIF orientation can be quite confusing if not handled properly. For example suppose you were using editing software that doesn't support it. The image would be oriented wrong. You rotate the raw file data and save, the EXIF orientation is preserved . Loks fine in the editor but when you view it in something that does support it now it's flipped again. LOL... That's worse case because the orientation is no longer accurate.
How this applies here is as I just mentioned in previous post the thumbnails are not handled by plupload. The EXIF data is stripped when thumbnails are created so they will always have wrong orientation if they are oriented with EXIF.