On the off chance you haven't I wonder if you have configured your content source to crawl complex url's?
Under the search settings -> Manage Crawl Rules -> new crawl rule
Just type in the host name for the website you are wanting to crawl and postfix it with an '*'. For example:
http://www.domain.com/*
Also, under Crawl Configuration, select the 'Include all items in this path' and tick the 'Crawl Complex URLS(URLS that contain a question mark(?))'.
Then just specifiy what account you want to use to crawl the URL and click on 'OK'.
You may have already done this already, but just on the off chance you hadn't.