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The main pages which are fine are like this:
The "extra" pages I have look like this (not sure if I'm allowed to put actual url in post?):
Is the question mark preventing SE from seeing any of these additional pages?
Help very much appreciated.
For the best ranking you wanna make sure they are directly linked from your main page and infact all your most important pages should all have links to each other.
Did you check with site:www.yourdomain.com command to see if your pages are indexed? maybe the sites are too similar and only a portion of them are being indexed for that reason.
But none of the extra pages of which I have about 50!
1) The pages that are not directly linked from main page would not get as good as a ranking vs. if they were linked from the main page.
2) Your problem is very common problem facing many. It is called the Sandbox effect, which is a new algorithm by Google. There are a few other threads about this. Basically Google is penalizing new pages or sites and not assigning them PageRanks for at least 4 months, maybe more...There are people here that have had no pageranks for about 6 months or so.
Nevertheless, you should look into the apache redirect command.
You also want to make sure that your site doesn't server cookies or session id's to search engine spiders. I believe the way to do this is to have a list of search engine spiders. Check for them each time a page is visited and don't serve the session id's or cookies.
With those three things (apache redirect for dynamic to static url's, no session id's or cookies) your site should look identical to a static site. You'll need a tech involved to get all this done though - and there are probably plenty of easier things to do for the engines before you get here (I was #1 in Google for my admittedly small terms while I was committing all three of the above offenses).