I have a static pages with dynamically expanding content that google is indexing. I also have deep links into virtually duplicate pages which will pre-expand the relevant section of content into the relevant section.

It seems like Google is ignoring all my specialized pages and not putting them in the index. Even after going through web-masters tools, crawling and submitting them to the index manually.

I also use the google API for integrating search on the site, and the deep linked pages won't show up. Is there a good solution for this?