Like others here, this a new problem from us. Only started after the new iOS was released.
On my Mac I have folder with photos. Those represent my Albums.
I use the latest iTunes to sync photos from "folders" to iPad.
Later on if we add a couple of photos and "sync" it shuffles images or doesn't add some.
Even if we clear the cache on the CPU.
The only solution I found is to delete all the photos from the iPad befroe you add any new pics.
The way we delete them is we make a folder with just ONE random pic in it.
Sync the one pic over so it deletes all the the other Photo Albums/Thumbs/Cache/ any other garbage in there.
Then Re-Sync all our Albums over as if the iPad was brand new.
I know this is a horrible work-around but it works until software is fixed.
It seems the way the photos are named when transfered to the iPad are conflicting with thumbnail names/cache that may still be stored in the iPad. Just a guess.
This really blows because we just got all our pics to show up in order by naming correctly and stripping Meta Data. Now, we are back to square one.....actually we are behind square one.