Savanadry - 1:24 pm on May 25, 2012 (gmt 0)
I have a very similar problem, in my case site A was the main site and site B was the blog / news section. Both different domain names but share the same nav bar and IP (set up over 6 years ago and all was fine until recently).
My theory is that google has realised the similarities between the sites and is assuming one is scraping or copying the other. In my case one ranked well while the other died, then the roles were reversed temporarily so it was pretty obvious one was knocking the other out of the serps.
I am in the process of combining the 2 sites onto the main site (moving news to the main site and 301'ing the old articles) which to be honest I knew I should have done years ago, I will report back here the results.