I too have got exactly the same issue and have been to the local Apple store. They tried viewing the pictures on the Mac and they were all ok.
As well as importing the files in the normal way I have opened them in internet explorer, via GMail and also firefox and get the same result everytime.
Even when looking at thumbnails I can see that they are upside down too.
Have you had any joy in getting this answered?
In my case I take HD video with an Apple iPhone 4S and an iPad 2. These cameras can be just as easily oriented in any of four orientations by hand, or in various iPhone or iPad holders for mounting on a tripod. As long as I stay with Apple or Adobe products for my whole video handling process, I have no problem with software support for orientation
While there are countless software programs available today that display JPEG images, only a subset of them actually interpret the EXIF Orientation flag. Just like color management, many programs simply display the JPEG image as it is stored, and completely ignore any extra details stored in the file's metadata. The most important of these additional details is the Orientation flag, stored in the JPEG APP1 marker under EXIF IFD0.
More explanation of this is in the text below.
Briefly, Apple is doing it right, with their iPhone 4S and iPad 2, the way most High end video cameras do it. And they made sure that their apps looked at the appropriate flag to rotate the image before showing it. To understand this look at this site:
This is a site that explains the whole deal. Apple and Adobe are looking at the flags for image rotation. Plex,and many others are not doing so. VLC for instance, DropBox is anpther example, Thunderbird is another example, the list is long.
Many newer digital cameras (both dSLR and Point & Shoot digicams) have a built-in orientation sensor. Virtually all Canon andNikon digital cameras have an orientation sensor. The output of this sensor is used to set the EXIF orientation flag in the image file's metatdata to reflect the positioning of the camera with respect to the ground. Canon calls their sensor the "Intelligent Orientation" sensor. It is presumably a 2-axis tilt sensor, allowing 4 possible orientations to be detected. The paragraphs below are taken from that wonderfully illustrated link.
Auto-rotation in Digital Cameras
While your digital camera may include an option to "auto-rotate images" due to the camera's orientation, this is almost always just a "virtual rotation". A flag is set to indicate to the viewing software / LCD preview which way to rotate the image before display, rather than rotating the image content itself.
As lossless image rotation is a fairly compute-intensive operation, digital cameras are not likely to include true lossless rotation after capturing the photo. The CCD/CMOS sensor hardware is designed to stream raw data in a particular direction (e.g. rows then columns), and so it may be hard to incorporate true auto-rotation in-camera without a performance impact to continuous shooting (frames per second).