Mail sending new message notifications for Old Messages

Hi,
Since upgrading to Mavericks I've been having a ton of problems with the Mail App.
I'm running on a Macbook Pro (13-inch Early 2011 Model) with 4gb of RAM and OS at version 10.9
I have Mail connected to two different accounts 1 Gmail and one Exchange. The recently released "Mail Update" has not fixed these issues.
The primary issue is that every time I have Mail open it constantly pops up notification badges to say that I have new messages. In fact it is sending these notifications for messages that are in most cases months old. Moreover even after confirming these the next day it will repeat this for the same exact messages. I've attempted to rebuild the index by deleting the Envelope files in the Library as suggested in another discussion topic. This didn't correct the problem. The result of this beyond the annoyance of having the notifications constantly popping us is it also seem to make my system grind to a halt - while it is parsing these sometime 100's - of notifications.
I believe related to this (but not clear) is that in many cases delivery of messages to my exchange account is very very delayed. I will receive a message on my iPhone Mail app sometimes hours before it syncs into my Laptops Mail app (even with attempts at Manually checking mail.)
Anyone have any suggestions on how to repair this issue?
Thanks a ton,
Mark

Try this:
Go into Preferences -> General and uncheck the box that says "Play sounds for other mail actions".
I'm not sure if it will work since that's really still "new" mail, but it might be worth trying.

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Mail sending new message notifications for Old Messages

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