While watching the ATV1 just now I noticed a new item listed under the 'Movies' tab.
It is 'Shared iTunes Movies', I clicked it and all my newer iMovie's sync'd, amazing.
I did the same with all the other heading tabs on the ATV main page and now my music, TV shows are all on the ATV1 in the proper order.
I do have 'Home Sharing' set up, which could explain this.
In the iTunes main page>Devices it still only shows Photos as available to sync but adding the other catergories direct from the ATV1 works, for now.
Maybe this will help someone else in the future.
You've set the iTunes library up as a secondary library (streaming only) instead of a Primary library. You can stream all your movies etc from iTunes, but without syncing them when you turn off the computer the movies etc will disappear.
You need to disconnect your library (settings > computers) and reconnect it as a primary library (settings > computers > connect to iTunes...... NOT add shared library)
I just found out that without the computer turned on that 'sharing' doesn't work, I'd messed up something for sure..
I followed your instructions and all the Sync Headers are now showing as before.
Basically it wiped the ATV1 and is re-setting all my data from the different headings in iTunes right now.
Thank you for your timely and accurate answer!