If you are using Windows Live Photo Gallery, you'll have to make sure that it is finished saving the changes to the actual files (instead of just saving the changes to WLPG's own internal database/to-do-list) before uploading the photos.
You can monitor WLPG's progress by paying attention to the little icon in the lower left corner of the window that shows the number of thumbnail updates, face scans, file updates, etc. remaining when you hover over it.
Note that JPG files have the actual pixel order and the orientation flag to describe which way is up.
Some programs don'tread the orientation flag and so will just show you how the pixels were read by the sensor at the time of capture. The only certain way of any given application truly displays the image right side up is to preview the images in an image viewer which ignores the orientation flag which in the image's metadata. http://www.impulseadventure.com/photo/exif-orientation.html