Make fancybox appear on top

Fancybox has it's own CSS file, and you should look for #fancybox-wrap and change it's z-index'es there. But anyways, it has pretty high setting by default (1101 on mine), therefore I'd suggest altering your own HTML/CSS.

Just in case, check if you have added that fancybox stylesheet in your HTML.

I've addded:

.fancybox-overlay {
    z-index: 1000000 !important;
}

in my stylesheet for recent version of fancybox.