I have the following code in my website:
<link rel="apple-touch-icon" href="http://website.com/images/apple-touch-icon.png" />
When I view the source in Firefox and click the href attribute the icon shows (so its not a 404 error).
When the code is added to a page like http://website.com/mobile/index.php or http://website.com/mobile/page.php and the page is added to an iPhone homescreen the icon works fine, but when the page url is like http://website.com/page or http://website.com/index the icon doesn't show up.
No errors appear in the "website debug console" provided in Safari options and I've tried clearing the cache and cookies.
Also I use the tag <base href="http://website.com/mobile/" /> website, which shows up on both http://website.com/mobile/index.php and http://website.com/index. But i can't see how that would effect it since the apple-touch-icon uses a full url.
Try using a relative URL:
<link rel="apple-touch-icon" href="/images/apple-touch-icon.png" />
It should go to your base directory and find the icon in /images.