Users getting 'flooded' with not read notifications (NRNs) for old emails and meeting requests

I'm being placed under quite a lot of pressure from senior management over a relatively trivial issue. Basically the vast majority of users are complaining that they receive not read notifications (NRNs) for old emails and meeting requests in large numbers multiple times a day. I know something strange is happening because some are delivered at silly times in the morning (i.e 3AM or 4AM).

The problem I have is that these some of these NRNs are from meeting requests and messages that are 120 days old, so some users have deleted the original message so I don’t actually know if the NRN is from an email or meeting request.

This is typical of what users receive as a NRN:

From: Sender 
Sent: 23 March 2012 04:16
To: Recepient
Subject: Not read: Accepted: Status update

Your message 

   To: Sender 
   Subject: Accepted: Status update
   Sent: Wednesday, November 23, 2011 8:59:00 AM (UTC) Dublin, Edinburgh, Lisbon, London

 was deleted without being read on Friday, March 23, 2012 4:15:32 AM (UTC) Dublin, Edinburgh, Lisbon, London.

...

From: Sender 
Sent: 18 March 2012 01:13
To: Recepient
Subject: Not read: Gold delivery - Sourcing module


Your message 

   To: Sender
   Subject: Gold delivery - Sourcing module 
   Sent: Friday, November 18, 2011 9:37:58 AM (UTC) Dublin, Edinburgh, Lisbon, London

 was deleted without being read on Sunday, March 18, 2012 1:12:37 AM (UTC) Dublin, Edinburgh, Lisbon, London.

I have done a search and found the following:

http://support.microsoft.com/kb/2544246

http://support.microsoft.com/kb/2471964

But we already installed 'Update Rollup 6 for Exchange Server 2010 Service Pack 1' back in December, so I am not sure what we can do to fix this?

BTW we are running Windows Small Business Server 2011