I had this problem about a week ago. My index page is optimized and ranks for the best keywords. When someone pointed out to me that my site didn't rank anymore, I noticed that all but my index page were stil ranking. For some reason my index page got de-listed completely (not in site: either) and after I sent through a reconsideration request, Google responded that they did not see anything wrong with the site (and then the index page mysteriously returned).
Must be a bug.