This happened to em when I was working on a movie site. Google deindexed 800 pages of mine leaving only about 200 index pages, but they automatically reindexed it in the next week. But the sad part is that my site never came up again to first page for some particular keywords. I think when google deeply notices our site they do this, just a blind guess though.
According to me you should - stop building back links for some time, maybe a week or two. Try to share your site in social sites in a very natural way, so that natural traffic comes to your site. Try to build some activity on or off your site.
Remember Google likes activity.... Read my other thread for more.... Maybe the activity part can help you sort out the problem
http://www.blackhatworld.com/blackhat-seo/white-hat-seo/385566-2-google-5-days-230-000-000-exact-competition.html