Two accounts in Mail

I have recently inherited a Macbook Pro from my boss who got a new one. He used migration assistant to transfer data and I reformatted the laptop completely to delete his username and data and start over. Now I am having a problem with Mail:
In my Mail I have two accounts: my account is set up as POP and my boss's email account set up as IMAP (so that his email can stay on the server for a week and it does not disappear when I open my mail). When I used a PC there was no problem - when I downloaded his email from the server onto my PC nothing occured to his email (if I deleted it, moved it to different folders that I had in my Outlook express etc).
However, now when we have two Macbooks Pro whenever his email is first downloaded to my computer if I delete it or move it it disappears from his Mail on his computer. It is as if the server "thinks" our machines are one machine. However, if he is the first one to download the emails this does not happen. Nevertheless, I cannot know where was email downloaded first - to my or to his computer - and therefore cannot delete or file emails to different folders.
I would really appreciate help since this is truly affecting my work. I have tried different setups in email accounts but nothing works. I even tried Outlook on my Mac but the same thing happens. Therefore, I belive that the problem is not in the email client but rather in the server or network, but I might be wrong.
Thanks a lot in advance!
Ana

Try unchecking these two.
AnaVila wrote:
I have move deleted messages to trash checked and permanently erase when One month old

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