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Old order emails being resent after upgrade to 1.9.3

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Old order emails being resent after upgrade to 1.9.3

I upgraded to 1.9.3 recently.  I tried to do it in magento connect but it kept saying module 1.9.2.4 conflicts with 1.9.3.  So I downloaded the new files and just copied them over the old 1.9.2.4 files.  It seems to have worked fine but All my customers are getting emails for orders that have already been shipped to them.   

 

Any ideas on how to check why this is happening and how to stop it.

Thanks,