I've been trading emails with Google Enterprise Support about this for the last month or so, as a client of mine had the same problem.

From an analysis of several emails that showed up as (Unknown Sender) in the Gmail interface but correctly in the IMAP client, it appears that the problem is in the email headers 'From' and 'Sender.' Google wants all of the necessary information to be in the 'From 'header, while it appears that some emails just put a name in 'From' and put the address in 'Sender.' This does not just affect internal MS Exchange recipients. In my experience, it affected a lot of old emails (say, from 1997 to 2004) and the only time an Exchange server was even in the picture was from about 2005 to 2009 -- and even then, there were only a handful of internal addresses.

The Google tech I worked with verified the problem and indicated that the best solution right now is Goolge Apps Sync, which is only available to Premier/Education Google Apps customers. He said that he'd also filed a request with the Gmail UI team to maike better use of the 'Sender' field, but that he couldn't promise that they would do it. I sent them several examples and we walked through all sorts of processes for transferring the email to Gmail (drag-and-drop from Outlook, Mail fetcher, transfering to an intermediary Mercury Win32 server, etc).

At any rate, Google is aware of the problem, so now it just remains to be seen what they'll do about it.