Actually, what you're probably seeing is the photos being uploaded in their original orientation. But most photo viewers, editors, etc. can use the built in EXIF information embedded in the image to display it correctly.
XF can display them correctly too, but it requires PHP to have the EXIF functions enabled. You can sometimes enable this within your hosting control panel. If not, then it's usually just a case of asking your host to enable those functions for you.
After that, any new photos uploaded we will automatically flip/rotate them according to the built in EXIF metadata.