Sorry this isn't an "answer," tho it is a response to the other comments here. This problem is just flabbergasting. It is very easy to isolate (i.e., has nothing to do with number of stylesheets), and doesn't have a proper "solution," as there is no way to achieve the desired rendering.
<!DOCTYPE html>
<html>
<head>
<style>
#container {
margin: 1em auto;
width: 40em;
}
#wrapper {
overflow: hidden;
position: relative;
}
#c1 {background-color: #aaf;}
#c2 {background-color: #ccf;}
.column {
float: left;
margin-bottom: -5678px;
padding-bottom: 5678px;
width: 50%;
}
#footer {
background-color: #eee;
padding: 1px;
text-align: center;
}
p {margin: 1em;}
</style>
</head>
<body>
<div id="container">
<div id="wrapper">
<div id="c1" class="column">
<p>This is some content in a short column. We would need some Javascript to change its height if we wanted a different background color for each column to stretch the full height of the respective columns...or we can use large padding together with an equal negative margin.</p>
<ul>
<li><a href="#p1">Jump to P1</a></li>
<li><a href="#p2">Jump to P2</a></li>
<li><a href="#p3">Jump to P3</a></li>
</ul>
</div>
<div id="c2" class="column">
<p id="p1">The desired effect is to have the height of the two columns appear the same. We use 'overflow:hidden' on the containing div (#wrapper) to wrap it around the floated columns.</p>
<p id="p2">These paragraphs have fragment identifiers. Problem comes in when clicking one of the links on the left. Instead of scrolling just the page, the browser scrolls the div with 'overflow:hidden' so the target is at the top. It does this even if the target is already visible.</p>
<p id="p3">Opera does not exhibit this behavior. This occurs in Chrome/Safari, Firefox, and IE. (Interestingly, IE also works as expected if we completely remove the DOCTYPE declaration.)</p>
</div>
</div>
<div id="footer">
<p>Footer stuff.</p>
<p>To see why 'overflow: hidden' (or any other piece of the CSS) is needed, just try disabling it.</p>
</div>
</div>
</body>
</html>