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Alright... basics.
When you take a photo, the bottom of the photo is down. Down is actually the bottom of the camera.
So when you turn your camera (your phone) sideways to take a photo... down is now to the side. The bottom of your camera is pointing left or right, not down.
Apple store a bit of info in the photo so that it can fix this when it displays the photo. The info says "The camera was turned to the side.".
When Apple displays the photo, the bits of the phone that deals with photos looks for that bit of info and says "If the camera was turned to the side, rotate the image when we display it.".
Flickr also does this, but only when you upload the file to them.
A lot... and I mean a hell of a lot... of software does not do this.
And this includes desktop web browsers.
In something like Chrome, when you give it an image that has "The camera was turned to the side"... Chrome just looks blankly at it, and then just says "The bottom of the camera is bottom... just put the photo on the page already".
Note that the desktop browser did not rotate the image according to how you took the image.
As some (very) large number of things will just ignore that extra bit of information, there is only one way to be sure everyone always views the file the right way: Rotate the image yourself.
If you edit the image and set the rotation, and save it. You're disconnecting a bit of the knowledge about which way the camera was rotated, and you're explicitly saying "This is the bottom of the photo.".
Nothing can get confused by that. And so your photos will always be the right way.
OK - that sounds way beyond my basic level of computer literacy... I think I understand parts of your post but the thin is one particular picture here: http://www.lfgss.com/comments/11756475/
was taken on a iPhone in portrait format - uploaded on to Flickr where it remains in portrait format, but as you can see switches to landscape once uploaded here - why would the exif data or software interpreting it get confused across the different platforms..? Again - looks fine on iPad and phone just on desk top is screwed up. (I had a similar problem in current projects where someone asked me how life was in Australia - pic looked fine to me but on desktop was upside down).
This is one of those mysteries - c'est la vie - sounds to me like a flickr prob.