Smart mailbox folders missing

That says it all. I created several smart mailboxes and then created several smart mailbox folders. When I close mail  and re-open, one smart mailbox folder remains and the others are gone, along with some but not all of my smart mailboxes. Any one got any ideas?

Came here looking for help with almost exactly the same problem. Made a couple of Smart Mailbox Folders yesterday (for the first time under Lion), and suddenly at some point today they're gone. Although I don't appear to have lost the 2 or 3 actual Smart Mailboxes they contained.
Thought maybe I'd imagined creating them for a moment, but took Mail into Time Machine, and there they were on all backups back to yesterday afternoon. TM will only restore actual messages I think ... so recreated the folders, but as you found, on quitting Mail and reopening, there they weren't - gone! Again!
And now, couple of hours later, I try again, just for the **** of it, and at the moment the one folder I've made appears to be staying put. Not aware of any particular difference in machine context, though clearly there must be something.
Some curiosities ... think I noticed they'd gone shortly after having a perplexing few minutes where I'd lost the Icons for my USB TM drive and a mounted DVD off the desktop, though they still displayed as mounted in Finder sidebar - nothing to do with Finder prefs, I checked and Finder was still set to display icons mounted disks; and at the same time, two particular documents (out of around 30 items) on the desktop that keep sporadically losing their positions repeated their offense. May have nothing to do with the Mail folder problem, but these are the first two head scratching moments I've had in my first 3 weeks of 10.7.3.
If anyone can shed any light on this, that'd be great.
Just getting to grips with a brand new Macbook Air, my first Intel Mac so I've leapfrogged Snow Leopard, but never had this problem with the few uses I made of Smart Mailbox Folders under Leopard.
Andy.

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