Hi ,
In addition to all the above suggestions ,Based on my knowledge i have also given some suggestions please have a look in to it.
1.To analyze this problem , first we need to do a message tracking for anyone of the duplicated message to find out where the message has been originated or else we can review the message id's on the headers of the duplicate messages to find out it is having
an duplicated message ID (i.e same message id for both the messages).But in some cases it might be triggered twice from the source .At the Same time in exchange by default duplicate detection is enabled and it will drop the duplicate messages copies with same
message id's and finally it will deliver only the single copy of the message to the user.
Example : Just think a user called nithya is sending an message to himself by marking an copy on the CC field and also to an distribution group mentioned on the To field .On such case just assume that distribution group that contains some members along with
that user nithya is also an member of that DL.
For the above scenario nithya will be getting only one copy of an message even though there would be an chance for the user nithya to receive two copies of the message.
2.Does this issue is happening for the emails which is coming from the external world or else for both internal and external messages ?
3.Does all the account which is experiencing this issue belongs to the same database else users was placed across different data