The link is http://tbldesign.net/affiliates and not just tbldesign.net, How do I fix this?

http://www.google.com.au/search?sour...en&q=tbldesign

http://www.google.com.au/search?hl=e...:tbldesign.net
it knows you are there.

But when you search "tbldesign" it comes up w/ tbldesign.net/affiliates.php and not tbldesign.net, how di I fix this?

You don't want your affiliate page to appear ot what? I can't find both your links in search results.

This appears on the first page, this not being my home page

tbldesign.net/index.php appears when you click "pages from", so it does know about you homepge. It just doesn't think it's worth listing it..

How long has the site been up?
You could try making a sitemap, this will encourage google to spider your site completely, and possibly list it.

Also, Your internal pages link to index.php, But (im guessing) your backlinks do not.
You should make all links, internal and external, point to the same URL.