Hi,
I have not read all of the posts above but I thought I would post what I did in case it was of any use to anyone. If this is old news then apologies.
Also, for the record, I think it's very poor that this problem exists and has not been addressed. The screen quality and display of photographs was a key feature for me when choosing to buy the new iPad and I am quite disappointed. I think it is important that people add their names to fora such as this so that Apple can see the size of the problem.
Anyway, I am using Windows 7 fully up to date with Windows Update at the time of writing. I was struggling to get past ten or so images onto the iPad. I tried syncing from a folder I had created on my desktop, which contained subfolders. I then took the images out of the subfolders so that there was only one folder containing all of the images. I then ran sync and predictably got a handful of pictures onto the iPad only.
Then, instead of deleting the iPod Photo Cache folders (all of those labelled F00, F01, F02, etc) I just deleted the Photo Database file at the bottom. Then I ran sync again and it topped up a bunch of photos whilst keeping the old ones on the iPad. I repeated this a few times and it did all of the photos in the folder. The number of photos it would add was unpredictable, sometimes tens sometimes over one hundred. I am only doing a few hundred in total as well; I guess if you were adding a lot this would become unworkable. However, I've done it twice now, removing all of them and retrying it and both times I topped them up to full.
Still, there are problems with the thumnails not matching each time and photos reappearing at odd intervals when scrolling through. And I have no working subfolders other than those that I make on the iPad.
Nevertheless, I now have something to look at... on the massively expensive retina screen that I spent hundreds on and which does not fit the purpose it was acquired for.
Thanks,