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It is not something that I have looked at closely before but it would seem that only pages that have been indexed by google are returned by the google site search (which when you think about it makes perfect sense). Is there a way to get google to index the whole site? or another option for site searches
Applologies if I have posted in the wrong area.
This because on young sites (submitted from a few time),so with low PR, is not easy to get all the pages indexed.
In a general way however you could verify trough the log file What are the non crawled pages and check the relative internal links to be sure that they work properly (prefer textual links) and as Google find pages trough links,you just could get inbound links on those pages.
Keep in mind that however is only a question of time.