How to sync mail accounts between iMac and iPad2 properly?
It sounds like the account type might be POP instead of IMAP. POP stores messages and all message attributes on each client (iMac, iPad, etc). IMAP stores messages and attributes on the server, so every client has the same view of the messages (including unread/read state). So, the solution for you is to use IMAP if the account supports it.