Well, with stuff on a subform, the browser doesn't have to request anything separately since the script is already on the web page. As for the "home page" -- if you mean the thing you have set to open with the database URL (via the database launch properties), then you're running into a base URL problem again. Let's say you have a database at the Domino data root. When you open that database, you're using a URL that looks like:
http://www.mycompany.com/database.nsf
If there are any relative URLs on the home page, they'll be looking for your JavaScript file at:
http://www.mycompany.com/myscript.js
The simple cure for homepagitis is to redirect your users to:
http://www.mycompany.com/database.nsf/
It's the trailing slash that makes the difference. Why are your images showing up? I'd guess that you created them either by using "Create>Image Resource" or pasted them in. In either case, Domino handles the relative URLs for you automagically.