Did you mistakenly set a Guide Layer? They don't render.
Yes I believe he is correct about the Guide Layer. The reason it is ok in the project, is because whatever variable you have input is not seen yet.
we need more information. what does your setup contain? what effects? what Ae and Os version? don't crop screenshots show us the whole Ae interface.
a quick guess: did you happen to use rotobrush to cut something out of the background? if you did, it's good advice to freeze your rotobrush strokes to make sure they register to the cache upon render - this can cause these type of problems if you don't.
more about freezing here: