I don't see "Term Store Management" in site collection settings. I checked this blog post http://blog.petergerritsen.nl/2010/06/09/term-store-management-option-missing-in-site-collection-settings/ which suggests to activate a feature which I tried but I still don't see the option. Is that something that I am missing?
Activating the features as above is normally enough to do the trick.
We came across the problem with a client after spending hours searching the web previously for the BCS, metadat, term store were not working even in the central admin. As a result we'd post here in case this of use as it is related.
hopefully this will save you some time too.