Just my opinion but I would stick with JavaScript

. If someone disables JavaScript then they will encounter many other issues more significant than having to close a splash screen (assuming they still can..). Besides, the page in question already uses a great deal of JavaScript.
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If you can do something both server and client side, it's always better to do it server side
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This is a very sweeping statement.. They are different tools and only overlap in certain specific areas (such as cookies).
I agree that coding cookies is easier in PHP, but not enough to make me chose to use PHP in preference to JS.