There is more good news for webmasters bugged with supplemental results issues. Vanessa Fox, Google Engineering updated about the testings at Google to resolve the issues. Here are excerpts from her post-
When you do a site: search to see how many pages of your site are in the index. We've been refreshing our supplemental results (you can read more about that in Matt Cutts' blog post) and this refresh has involved some serious changes under the hood. Unfortunately, with change of this scale, there sometimes are bugs. In this case, we found a few bugs that affected the site: operator. Some particular ones you may have noticed are that the following types of queries don't return the correct number of results:
site: queries where you type in a trailing slash (such as site: www.example.com/)
site: queries for a domain with punctuation (such as site: www.example-site.com)
In the meantime, site: queries without the trailing slash may provide a better result.