Everyone with the index problem, here is the fix, replace extra/index_links.php with this:
Code:
<link rel="stylesheet" type="text/css" href="/app/tpl/skins/Project Habbo/styles/index.css">
<link rel="stylesheet" type="text/css" href="/app/tpl/skins/Project Habbo/styles/navigation.css">
<script type="text/javascript" src="http://code.jquery.com/jquery-1.7.0.min.js"></script>
<script type="text/javascript" src="/app/tpl/skins/{skin}/js/jquery.tooltipster.min.js"></script>
<link rel="stylesheet" type="text/css" href="/app/tpl/skins/{skin}/css/tooltipster.css" />
Goodbai! 
EDIT: I see he fucked up Register too, place this in extra/register_links.php
Code:
<link rel="stylesheet" type="text/css" href="/app/tpl/skins/Project Habbo/styles/register.css">
<link rel="stylesheet" type="text/css" href="/app/tpl/skins/Project Habbo/styles/navigation.css">
<script type="text/javascript" src="http://code.jquery.com/jquery-1.7.0.min.js"></script>
<script type="text/javascript" src="/app/tpl/skins/{skin}/js/jquery.tooltipster.min.js"></script>
<link rel="stylesheet" type="text/css" href="/app/tpl/skins/{skin}/css/tooltipster.css" />
EDIT again: Seems like that didn't fix the register page as a whole, login boxes are still appearing on the wrong places, although with the code above it looks less fucked then without :P
Workin on it.