When in the "unified folders" view of Thunderbird (5.0 Linux 64-bit, but also noticed on previous releases on both Linux and Windows 7 32-bit and 64-bit), it frequently happens that a message is put in several folders at once. As an example, spam appears both in the "All mail" folder and in the "Spam" folder.
With my (GMail-based) IMAP accounts, when this happens, there are various display refresh problems associated with it. For example...
-An unread spam message that's read and deleted in the All Mail folder still appears as a "ghost" unread message in the Spam folder, until I visit this folder and briefly see it before it disappears.
-When I receive spam on one of my IMAP accounts, it does not always appear directly in the unified Spam folder. I have to explicitly open Spam->AccountName before I see it. Which is strange, because this never happens with the unified inbox.
-The same also happens with sent messages. Sometimes, newly sent messages are not put in the unified Sent outbox, I have to explicitly visit Sent->AccountName before this happens.
-With previous releases of Thunderbird, messages sent from IMAP accounts sometimes didn't appeared either in the unified Sent folder or in the Sent->AccountName folder, although I could perfectly see them on my webmail. But it's not all the time, I've not yet seen it happen on this release, and I don't know how to reproduce it.