I dont know if this is any help to you but it goes through step by step, maybe you could re-go through the steps to make sure you havent missed anything out?

http://fabiangwilliams.wordpress.com/2010/05/30/understanding-managed-metadata-in-sharepoint-2010-its-impact-on-taxonomy-navigation-and-search/

and for clarity of managed meta search crawl

http://technet.microsoft.com/en-us/library/ff621097.aspx

hope its so what help to answering your question!