What’s the difference between <a href="url"> and window.location = "url" on iOS?

I have an HTML 5 app that runs on mobile devices including the iPad. I want to create a link to a non-HTML file, and have the proper application open to handle the file. The files are .acsm files, to be opened in Bluefire.

If I create the link as a simple <a href="url"> tag, it works.

If instead I use Javascript to set the window.location, it doesn't work. The iPad pops an alert that says, "Download failed: This file cannot be downloaded".

I've experimented with other file types, and haven't found anything conclusive. What's the difference between the simple link and the Javascript technique? Can I make the Javascript code do the same thing as the link?

In case the specific Javascript details matter, I do it like this with jQuery:

$('.native-launch').live('click', function (evobj) {
  var there = $(evobj.target).attr('href');
  window.location.href = there;
  return false;
});

and the HTML looks like:

<span class="catalog-list-button native-launch" href="url">Read in another app</span>

(Note that this is a span with an href, I can change the HTML if that would help.)