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What quicksand does (in order to animate elements when reorganizing visible structure) is cloning the elements and injects copy of those into the DOM. Any events attached to those elements are gone after shuffling is done. This is why fancybox didn't work for those elements.
The way to fix this is described in quicksand plugin documentation (section "Integration with other plugins"). It involves passing a callback function to quicksand as a second element. That callback will be executed once the shuffling is done, in our case it will be responsible for finding and re-applying fancybox to elements that were shuffled.
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