More guesses for me.

Right click the account name in the folder pane. Select subscribed check the list of folder names in there is the same as appears in your account settings and on the folder tree.

I am guessing that the server calls Junk SPAM and trash deleted and such like.

When offline Thunderbird has no refence to check so does as it is toild and has trouble syncing letter.

Confirm the folder names used are consistent, using the server list as the "correct" list that is the list in the Subscribed dialog.

Matt:

First, is the list of mail folders and news groups for offline use the folder tree you are refering to?

Which of these two images shows the prodecure to select a folder on the IMAP server rather than localy?

- Jim

Jim, I said right click the account in the folder (that is the list on the far left of your screen) when you select subscribe you get a dialog that looks like the attached image. That is "what the server has" So you checking the other dialog for mismatches. You will also need to look in Server settings for your deleted folder setting. For some reason it is not with the others.

If you click on the advanced button in Synchronization and storage, you will get the same "subscribe" dialog if the other instructions just don't cut it.