Apple Mail Rules dont apply when mail is READ on other devices!

Hi,
I use IMAP settings on Apple Mail (v4.5) and also check my emails on the iPhone (iPhone also set up with IMAP). However if i have read an email on the iPhone then when i switch my computer on the incoming Apple Mail Rule that applies to that sender does not seem to work. It keeps the mail within my Inbox and does not transfer the mail/message to the desired folder.
However, if the same sender sends me an email which i do not read on the iPhone and then switch my Apple Mail ON, then the mail is automatically transferred to the desired folder.
It looks like the problem is only with READ mail and not UNREAD mail. 
Is there a fix for this? There seems to be a lot of people having the same issue and was wondering if there is any work around on this?
Would really appreciate any help from anyone on this.
Regards,
Jay
PS: I recently moved from Outlook 2011 on MAC to Apple Mail as i heard is a far superior mail application and works smoothly. So far everything about Apple Mail has been correct, it is a fantastic app, however this Rule problem is pretty basic and surprised that Apple still has not fixed this.

Hi Glenn,
Many thanks for this. Unfortunately i dont have this facility on the server as we are using a simple opensource mail delivery and storage service, so the rules would have to be set up on the computer.
I was using Outlook 2011 and prior that was using Entourage 2008 and both worked well with the IMAP rules. Nothing was ommitted and everything READ or UNREAD was imported and the rules applied. It's only in Apple Mail that these rules dont seem to work.
Is there no other work around? No Apple Mail Add-Ins? I see quite a number of people complaining about the same problem and i'm surprise that Apple has not found a solution for this.
Anyway, thank you soo much for your reply. Much appreciated.
Regards,
Jay

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