Sorry for my ignorance to read the first posts properly.
I was not able to figure out a way to solve this as it is.
But if those transitions arent super important to you, you could use
css to assign top with !important and then remove transitionIn and
transitionOut from your fancybox trigger. Then there would not be a
problem because that transition from thumbnail to big image wouldnt
exist anymore and the image would fade in into the position that is
set.