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I'm with Ryan - old data. I'm theorizing here, but think it has to do with the way Google reports queries. They say they report the top 2000 queries that resulted in pages from your site being displayed in results over the reporting time period which is, by default, 30 days. They're reporting the top 2000 query-page-result combinations. Since the redesign, you've had both old and new pages displaying in results so the number of query-page-result combinations could have as much as doubled, depending on how many of the new pages are indexed. It could take a while before you see impressions start to rise again but I think it's a reporting problem and not a visibility one. My two cents.

Hi Ray, Thanks for responding, I don't know my programming too well, but from the way you are saying it, it seems like this is a standard process. I will send this to my developers, thanks for your help!

Stephen, The flatter the architecture, the more apt pagerank is to reach all the pages of your site.  However, that has to be balanced with navigation that helps visitors most easily get to where they want to go on the site, which typically runs counter to presenting them with completely flat navigation. If you think of giving visitors fastest access to the content on your site that is most important to the majority of them and then require somewhat more numerous clicks to get to less important info, you'll probably do OK.