Flickr will automatically rotate photos based on information in the EXIF file. However if you have manually rotated a photo in some application that doesn't then also remove this rotational information you can end up rotating it twice, once manually, and once when Flickr gets it.
You can edit the preference here: http://www.flickr.com/account/prefs/autorotate/
This has nothing to do with the Flickr API or the .Net code though, so I'm not sure why you have asked it here.
Sam