Mail find/search not working

I have found that Mail has gone a bit bonkers. First I lost a bunch of important emails when moving the messages to a different mailbox (they are simply gone). Now the find/search function is completely erratic. The same search terms will sometimes turn up messages, sometimes nothing.
I have deleted the preferences, rebuilt the mailboxes multiple times, even deleted the envelope file so mail would rebuild the entire index from scratch. Also I've repaired permissions. The search function is simply erratic still.
I even had an issue after deleting the preference files where the custom tool bar would revert back to the default one when starting up Mail again... a reboot (and perhaps running various scripts through Onyx seemed to have nipped that one in the bud).
What is going on here? Anyone else havinfg these issues? How to fix it?
I am running Mavericks, OS X 10.9.1

... no fix for this problem?

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According to your description, my understanding is “find an item” search box in a custom list not work in your environment.
As search box and “find an item” search box in your home page are working, so the search service application is working.
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