Do duplicate ID values screw up jQuery selectors?

Element IDs are supposed to be unique. Having multiple DIVs of the same ID would be incorrect and unpredictable, and defies the purpose of the ID. If you did this:

$('.myDiv').fadeOut();

That would fade both of them out, assuming you give them a class of myDiv and unique IDs (or none at all).

"Note: I know duplicate id's is against standards"

Then don't do it. You have already figured out two problems. It violates standards, and it interferes with jQuery's (and indeed the regular DOM's) selection mechanism. There will probably be more issues in the future.

Quite possibly, you are using fancybox wrong, in which case I hope someone familiar with it helps you. Or worse, if the script itself is flawed, you shouldn't use it.

jQuery matches exactly one element when querying for an ID. An array of at most one Element object will be returned by $("#foo").get(). See the jQuery documentation for more information, or try it yourself.

$(function() {
    alert($("#foo").length);
});