I'm finding that W3 Total Cache is breaking my Fancybox functionality. Curiously, the problem isn't coming from the js file, but rather the CSS file.
The problem happens if I let W3TC minify the CSS file.
I can fix the problem by holding back:
from the list of minified CSS files. I can minify everything else and still have proper functionality, but when I minify this CSS file, Fancybox doesn't work. (Clicking on an image which should appear in Fancybox makes the image appear at the bottom of the page, not in an overlay, and throws a JS error.)
I don't know if there is a fix for this, but my work-around (not minifying that CSS file) might help someone else.