Jill Whalen discovered through several site audits that Google appears to have merged the index page with the root page of the domain. In other words, if your www.domain.com was the same as www.domain.com/index.html and you still linked to www.domain.com/index.html, Google is now seeing these pages as one and the same versus in the past where they would treat them as two separate pages and even split toolbar PageRank.
It may be an issue of the duplicate content filter on Google finally kicking in, which can take awhile, according to forum member Ron Carnell.
However, Jill has noticed it on the last five site audits she performed, so it's possible that it's something that Google is now putting into effect -- at least for now. Ron mentions that Google has once merged www.domain.com and domain.com but then unmerged it, so it may only be a temporary change.
Forum discussion continues at High Rankings Forum.