Thanks for all the useful replies here. The website OSX Daily has a comprehensive trouble shooting list article written back in June of 2013 that was also useful.
One thing I found that worked for me was to turn off the Restrictions for Movies by Ratings on my (kids) iPad. I had set them up to only be able to see PG rated films, and everything was working fine. However upon tweaking the library a bit - updating cover art and moving a few TV shows around etc, I found a heap of movies would not transfer across.
When selecting "On This iPad > Films" within iTunes, the Movies were there but greyed out with a circle next to them.
Tried everything else, and then removed the PG restriction on the iPad - BOOM - everything synced across.
If I can ever get the iPad back from Miss 3 who has sworn never to let Daddy play with it again, I'll let you know if the restrictions can be put back...