New Smart Mailboxes Disappear (again & again)

There are two smart mailboxes setup in the "Mail" application on my desktop Mac ("All Mail" & "Newspaper"). These mailboxes also exist on my laptop. On my desktop, I deleted the "Newspaper" mail box and created several new smart mailboxes. The next time I looked, the new mailboxes "self-deleted" and restored the "Newspaper" mailbox. I tried this several times with the same result. I then created a new smart mailbox on the laptop and deleted the "newspaper" mail box. Same thing happed; the new mailbox disappears and ther "newspaper" mailbox returns.
I use use IMAP with my Gmail account and forward my "iCloud" mail to my Gmail account. The "Mail" setting is "checked" in my iCloud system settings (but not sure what impact that has on my setup).   I thought this setting may allow the smart mailboxes to synchronize between the Mac and possibly my iPhone. I am using OS X 10.9.3. I recently returned to mac "Mail" after several years of simply using the Gmail web interface on the Mac (plus iOS Mail) and am a bit unclear how the iCloud sync should work. I am pretty happy with the newer IMAP capabilities after using POP in the past.
Any suggestions on how I can create (and keep) my smart mailboxes?
Thanks,
Dave

WHAT DIDNT WORK for me:
I have the problem, but I never had Docs & Data switched on, so Sheppard's solution does not apply for my case (there are no such files as mentioned there). Neither did Beda's move work for me. Causing fresh copies of the two files he mentioned to be created does bring back the Smart Mailbox category and a default Today smart mailbox, but putting the original files back in position, puts the problem back to square one -- no smartmailboxes appear.
WHAT DID WORK for me:
What I found worked was moving smartmailbox specifications from SmartMailboxes.plist into a clean SyncedSmartMailboxes.plist file.
Steps: (This procedure requires something that enables you to open and edit plist files (e.g. Xcode). As always, keep safeties of everything before you mess around.)
0) Before starting, check this file and confirm your smart mailbox specifications are actually still in there. If not, this won't work.
    ~/Library/Mail/V2/SmartMailboxes.plist
1) Taking a tip from Beda, move the following files out and then launch Mail and quit it, to force creation of new copies of these files.
    ~/Library/Mail/V2/SmartMailboxesLocalProperties.plist
    ~/Library/Mail/V2/SyncedSmartMailboxes.plist
2 ) Open the new SyncedMailboxes.plist. It contains a single item (a default Today smartmailbox specification). Delete that.
3) Open your SmartMailboxes.plist. It contains a sublist called 'mailboxes' where all your smart mailbox specifications reside. Copy each of these items over to (the top level of) SyncedMailboxes.plist. You have to do this one at a time if you are using Xcode, because there is no multiple selection available.
4) Save and close SyncedMailboxes.plist (and close any other plists for good measure).
5) Launch Mail and your smart mailboxes should be back.
Hope it works for you as it did for me.

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