I had the same problem, but thought it was strange because some of my old photos were being displayed on my iPad with the corrected orientation as shown/corrected on my PC, however some of the recent photos I had taken would only show as landscape on the iPad even though rotated and set to Portrait on my PC.
I have always used plain old Microsoft Picture Manager (MPM) to sort and correct the display of my photos and then Photoshop to make and changes if needed, I remembered that somewhere along the line recently my laptop had started using Windows Photo Gallery to open my pics instead. I am not sure why it had changed, probably something I had clicked on or agreed to by mistake along the way, and I regulary had to right click a photo to select Open with Microsoft Picture Manager to modify it with tools I was familair with, but this made me wonder if this was something to do with why some pics from a recent holiday were displaying correct and some from the same holiday and same camera where wrong.
I have tried opening them again in MPM and re rotating then re-saving but it doesn't recognise any changes so this didnt work. I reopened in Windows Photo Gallery (WPG), rotated again, resaved and re synched and yes this worked, but as I prefer MPM I tried other ways to re save in this program and found that if I opened the Folder in Windows Explorer, set the files set to display as Medium icons from the Views option on the Toolbar, then right clicked each photo that displayed wrong on the iPad, even if it was correct on the PC, then selected Rotate Clockwise or Counter Clockwise from the Right Click menu then I re synched my iPad and they are all now fine. You can eve use the multiple select tools of shift + click or Ctrl + click to modify lots of pics in one go.
So it has got to be to do with the program used to rotate and save in the first place!
Hope this helps someone, it has certainly made my day!