Same problem here as well... But, I have figured out the cause of the problem, but not the solution.... I tried several different things listed here (pictures that were taken sideways is one, it being all pictures taken is another, and it being the icloud photo stream is another) but for my phone at least these problems are not the bug.... I never turned on the photo stream option. Something about pictures of my children out there in the nether worries me... The new photo edit option within the iphone's default photo app is the problem... No matter which orientation the picture is taken from it will work just fine once you transfer it onto your computer, unless you have used the crop or auto enhance button with the phone. That is the option that screws up the metadata. If these pictures are emailed after that it will not cause a problem, but if they are transferred through the cable straight to the computer then they cannot be edited within normal programs (this includes the easy to use right click to rotate button). I tested this with several different options
Test set 1
One untouched photo taken with regular orientation
One cropped photo taken with regular orientation
One auto-enhanced photo taken with regular orientation
One cropped and auto-enhanced photo taken with regular orientation
Test set 2
One untouched photo taken in landscape mode
One cropped photo taken in landscape mode
One auto-enhanced photo taken in landscape mode
One cropped and auto-enhanced photo taken in landscape mode
Both untouched photos from test 1 and 2 worked fine. They could be rotated and edited without a problem. All other pictures from both tests could not be rotated or edited, and all had metadata issues.
I just finished the update to iOS 5.1.1 and tested it, this is still a problem... I am not sure how to fix this problem, I read some options on this thread that seemed to help for some and I may end up trying those. This is a very frustrating issue and apple really needs to get a jump on it.... This has been a problem since December? With as many people on this thread that have been having the same problem you think they would have fixed it by now.