List view status of flagged messages in Yosemite Mail Smart Folders

I'm using Mail in Yosemite with an Exchange server. Before Yosemite, everything was fine, now I have an issue with message flag status in Smart Folders. I have a Smart Folder which is my "ongoing" mail folder; it is set to only show unread and/or flagged messages. In the latest version of Mail, setting the messages flagged status does not change the flag icon in the message list, but does in the header of the actual mail message. The only way to get the flag to show up in the list is to select another folder and then reselect the smart folder. It does this on both my MacBook Pro and iMac, with with the latest Yosemite version and all updates applied.
In the previous OS X Mail (Mavericks) changing the flag status would remove/add the flag icon in the message list pane; now it doesn't. It's insanely annoying.
Anyone else seen this bug? I have tried recreating the smart folder and that makes no difference, neither has rebuilding the mailbox/deleting index/envelope file. No changes have been made to our Exchange server.
Cheers
Matthew

Well, I guess those are more "smart inboxes" and not "smart mailboxes" in iOS...

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