Leopard Mail fails to update IMAP server properly

I'm wondering if anyone has managed to see this problem and/or troubleshoot it.
System: Apple Mail 3.5 running on a MBP running OS X 10.5.5.
Scenario: When an IMAP email is received in the Inbox and moved to a folder 'On My Mac' in Mail.app for filing, then webmail and iPhone simultaneously recognise that the email has been received (as they should do) and the activity viewer in Mail.app shows that a message is sent to the IMAP account 'changing flags' which results in the email in questions showing 'as read' in the iPhone or in the webmail client.
However, the problem is that the email doesn't appear to be moved out of the Inbox when it should be. In fact, if the email is moved to a sub-folder of the IMAP Inbox in Mail.app, then it appears in the webmail client / iPhone as being BOTH in the Inbox and in the nested sub-folder.
In order for the correct email filing / moves to be reflected, we've found that certain things cause some different activity to take place between Mail.app and the IMAP account. For instance, if you click on any of the other folders associated with the IMAP account in question (e.g. Sent, Trash, Junk) then the email is immediately moved successfully on both of the other platforms using the IMAP account (webmail and iPhone), so there must be something achieved by clicking those parts of the account which clicking in the Inbox doesn't do. Quitting Mail.app also runs some script which achieves the proper sync of mail messages between Mail.app and the IMAP account.
Troubleshooting: Apart from the slightly inconvenient workaround mentioned above, I've tried a host of things to fix this problem. I've deleted the Mail.app caches from the ~/Library/Caches. This didn't fix it. I also have run Onyx to delete system-wide caches. I've tried changing the frequency at which Mail.app contacts the server, testing it at 5, 15 and 30 minute intervals. None of these changes have made a difference. Nor has turning IDLE support on and off in Mail.app. Finally, I tried to use a third-party plugin (Imapcheck) for Mail.app which offers to poll the IMAP server more often to see if this could overcome the problem (it didn't work).
All I can see that's left is to remove the IMAP account from Mail and re-add it. If anyone has any other ideas, I would love to hear them. Thank you in advance!

Sometimes iPad doesn't update emails. WiFi is strong. I use two places for conection and it sometime works, sometyme not -at bouth of places.

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