The following is pure, unsubstantiated gossip. With the jockeying for positioning going on as Lehman leaves and a new Commissioner comes in, some of what I am being sent probably is internecine undermining, a fun form of DC politics as Newt just found out. Regarding the email you referred to by Jack Harvey wanting the Microsoft files. Microsoft got the internal file wrappers turned over to them.
Examiners speculate that there was something damaging in one or more of the applications.
Something that would blow their defense out of the water in the Department of Justice case. So Microsoft retrieves the file wrappers, changes the damaging application and returns them to the Patent Office with no one the wiser. Evidence disappears, never to be seen again. Remember Lehman was a Microsoft lobbyist and that Microsoft is in a major lawsuit with the Department of Justice. Still I am Bayesian, and my source has been right in the past.