Yosemite mail flagged mailbox

I had my flagged inboxes named according to my preferences in Mail when I was running Maverick. E.g., the red flag had ben renamed "Critical".
Now, every time I start mail, the flagged mailbox revert to the original name (e.g., "Red"). If I try to change the name again, it automatically puts up the name I had originally given in the edit field (i.e., "Critical" for "Red"). So I can rename them all. When I quit mail and get back in, they are all back to their default names. This is very annoying as I had set up a number of key-commands to automate some actions.

Thanks yes I did look through there. There is an option to uncheck 'include related messages' but when I uncheck it it doesn't appear to stop mail appending messages to older ones?
I don't actually mind mail appending messages provided it puts new ones at the top of the mail box when a new one comes in. Its having new mail not flagged as such and not at the top of the mail box which is annoying
I've been using 'sort by date' as you would think that would have the most recent emails at the top, only it doesn't. So I'm now trying using 'sort by unread'

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