I had this problem. I had to contact google for 3 months, but i'll try to help you in 3 minutes lol.
1. Be sure your registered for google, you have to sign-up and wait for them to actually start indexing you.
2. Check the logs, are they trying to access or just hitting the robots.txt and index page?
3. Are they dynamic links? My site has this problem... I have one page load... and in that another page is called up (A dynamic page), this page isn't read by google, they only read the page it requests, not what other pages are called. You have to have static links that are right on the page that google is looking for, mine always hits index.php so I put links there and it went through to them.
I see the links, but I don't know if they're on a static page, and I don' know the last parts of it. Google told me if I say anything about "php?" in the code then i'm probably not going to be indexed.
If your signed up, then check the robots.txt and make sure googlebot has access to the site. Then make a site map page with all the links to the other pages and make a link to it in the index.php, I have mine hidden at the bottom and just says "Site map (mostly for web-crawlers)" and it's setup in a simple manner for google and users to understand.
If this doesn't help I can give you a link to google tips and the e-mail address to the googlebot department.