Inserting Javascript on main page won't work but individual pages will

I'm trying to insert this piece of code into the theme

<script type="text/javascript" src="http://www.avantlink.com/ale/ale.php?ti=401"></script>

At first I tried using the HTML/CSS Inserts and inserting it into the header and/or body bottom but that only worked on individual posts meaning that it was only active when you clicked on a single post and were viewing a single post.

I then tried following these directions

http://www.avantshare.com/blog/2008/...ordpress-blog/

and installing it at the end of footer.php before the closing </body>. I ran into the same problem.

I then tried inserting it into header.php and it once again only worked on individual posts. I am using firebug to troubleshoot and the odd thing is I that the code doesn't even show up in the header in firebug on the main page but it shows up fine on individual posts.

I should also mention that the script works fine when I click on Older Entries and view multiple posts that are not on the front page.

Is there a separate header file for the main page or is there another way that I can enter this script on the main page?