Background: When used as an IMAP client against Gmail, Thunderbird 3 (may be the case in v2 also, not sure) will refresh it's list of folders (the folders correspond to Gmail labels) when you do "Download/Sync Now…" or restart the Thunderbird client. Any new folders (labels) created in Gmail will sync to the client and any folders moved/changed/deleted folders in Gmail will move/change/delete on the client as well. (Note: Thunderbird has the concept of "subscribing" to IMAP folders (assumingly allowing you to determine which folders you want, rather than bringing all of them down and dragging loads of data across the wire). When used against Gmail, Thunderbird appears to automatically subscribe to all folders (including when folders are newly created in Gmail), so this might be why the refresh is happening properly.) This behavior is what I want with Exchange.
When using Thunderbird with Exchange (2007), the folder list doesn't refresh when folders are added/changed/deleted on the server and/or from a different mail client. When I look at the subscription options, some are checked and some are not (not sure why Thunderbird picked some and not others). And when I add new folders on the server and/or from another client, they never even appear in Thunderbird's list of folders, preventing me from subscribing to them.
Best Answer
The subscription idea with Thunderbird doesn't really work too well if you modify your folders outside of Thunderbird.
My suggestion would be to turn off subscription for that account altogether. Go to Account settings -> -> Server settings -> Advanced -> untick "Show only subscribed folders".