Found the above article that describes my issue.
We are using shared folders in Exchange2013. When you reply from the shared folder it is sent from the shared folder but the reply is saved in the sent folder of the primary exchange account in outlook. We are using outlook 2010 and 2007. In the article it mentions that the ability to have the sent mails save in the shared folder it was sent from does not exist in Exchange 2013. Is there a work-around to accomplish this?