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?

The problem "magically" resolved itself. No idea how. If there is a better solution rather than putting it in header.php I'm all ears.

I'd follow the suggestion of the Javascript author regarding the best location, there is no single best location for Javascript. Some recommend to put Javascript at the bottom, before the closing </body> tag so it won't delay the page load. The site might load faster, or at least appear to do so.