Why doesn't Mail empty Junk folders at every quit?

I select "empty Junk at quit" but still Mail doesn't empty those folders at every quit. Anyone know why this happens?

This is still happening to me with Mail v6.0 (1485) after updating to Mountain Lion.  I have to quit and restart Mail after resuming from sleep to get it to connect to any of my accounts.  One iCloud and one GMail account.
I have tried starting from scratch by removing all accounts, files in my Library ("Application Support" and "Caches" folders) and cleaned up my keychain, but still the problem persists.

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