Try deleting the photo cache from your computer and then re-try the photo sync and see if they then copy over into the correct albums - the location of the cache, and how to delete it, is on this page http://support.apple.com/kb/TS1314
There is a serious fault with the iPad 3 syncing large(anything taken with a good digital camera) photos using iTunes.
You are not alone - google it and check as there are many threads in this site about it.
I am returning my iPad 64G G4 over this very issue.
Apple tech people can't help as probably a hardware issue.