Have you subscribed to all the folders in Thunderbird?
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Ehm im not sure what you mean by that? I have the folders Inbox, Drafts, Templates, Sent, Archives (containing another folder), Junk, Deteled, Archief (self made I think), Notes, Outbox. Or is that not what you mean?
Right click on the account name. The folder above the Inbox folder in bold. Click 'Subscribe...'. Make sure the right account is selected at the top then hit 'Refresh' on the right side. Now you see a list of all the folders exist at the server and only when a tick is in front of it it will be shown locally. If a folder is unchecked select it and choose subscribe. Maybe the message is in a folder Thunderbird wasn't subscribed to.
Sometimes Thunderbird has a separate Junk folder besides the server one.
right I see. Apparently I am subscribed to all online folders. Considering it only happens SOMETIMES, this seems to perhaps allude more to a bug I'd say. Any other possibilities? I'm just unlucky?