First, make sure that the source page and the target page are both served through the file URI scheme. You can't force an http page to open a file page (but it works the other way around).
Next, your script that calls window.open() should be invoked by a user-initiated event, such as clicks, keypresses and the like. Simply calling window.open() won't work.
You can test this right here in this question page. Run these in Chrome's JavaScript console:
// Does nothing
window.open('http://google.com');
// Click anywhere within this page and the new window opens
$(document.body).unbind('click').click(function() { window.open('http://google.com'); });
// This will open a new window, but it would be blank
$(document.body).unbind('click').click(function() { window.open('file:///path/to/a/local/html/file.html'); });
You can also test if this works with a local file. Here's a sample HTML file that simply loads jQuery:
<html>
<head>
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.5.0/jquery.min.js"></script>
</head>
<body>
<h5>Feel the presha</h5>
<h3>Come play my game, I'll test ya</h3>
<h1>Psycho- somatic- addict- insane!</h1>
</body>
</html>
Then open Chrome's JavaScript console and run the statements above. The 3rd one will now work.