If a sent or received email has the sensitivity set to anything other than the default (ie personal, private or confidential), when the email is tracked the email bosy is blank and instead there is a .msg file attached containing the full emaill text. We raised this with Microsoft directly (case 113120310994696) and they told us that this was to do with a change made between Outlook 2007 and 2010/2013. This occurs in CRM4 and CRM2013.
The sensitivity setting should not affect how the email message is stored. With the current implementation, you cannot search for message text in advanced find. Furthermore, the message is not really hidden because users can always open the attachment.
Also, we have no control over received emails - if it's received as confidential, there's nothing we can do to ensure that the full email is saved as normal when promoted to CRM.