Hrm.. I thought perhaps this line might be missing,

$REMOTE_ADDR = $_SERVER['REMOTE_ADDR'];


if it isn't ... I don't understand why it isn't working correctly.
I see that out.php is working correctly, so I know your server makes the necessary environmental variables available to in.php... maybe after some more coffee I'll think of something but right now, it escapes me.

The ID a site is assigned, or rather the process of assigning an ID can vary depending on whether you are entering the sites yourself via the admin panel, via the public "add site" page and whether you have manual validation enabled or not.

If you are adding the sites yourself, I recommend doing so from the admin panel.

If you accept public submissions I strongly suggest you enable manual validation.

When manual validation is enabled, a submitted site's data is initially stored in a temporary table. Once the site is validated from the admin panel the data is moved to the actual links table and a valid site ID is assigned. An email is sent to the email address associated with the approved site containing the newly assigned site ID.. well at least it should.