Did you right-click the account in the Folder Pane, Subscribe..., Refresh, and see the folders in the list, and if so, subscribe to them?

Hi, thanks for you reply. Sadly the folders do not appear when I hit refresh.

The fact it happens on multiple machines suggests there's something at the server end that isn't getting through to TB, although it's working with other mail programs. What happens if you create a new folder through webmail, copy messages from the invisible folder to the new folder, then subscribe to the new folder in TB? Not a solution, just a workaround.

Is there any chance the missing folders have been quarantined by an AV program?

Well, I went through the hotmail web interface and renamed every folder that wasn't appearing in Thunderbird, then from within Thunderbird I created new folders and used the hotmail web interface to move all the emails from the old folders to the new ones. I then deleted the old folders, and everything is now working as it should. Fingers crossed it won't happen again.

Microsoft have never bothered to fix some serious bugs in their IMAP and POP implementations. Perhaps a motivating factor is they want you to buy outlook and use that as it does not use IMAP or POP. Instead a Microsoft proprietary protocol.

But regardless of the reasons the Microsoft IMAP implementation is quirky to put it nicely.

I've NEVER been accused of being nice to Microsoft/Windows/Hotmail/Live/Outlook.... for simplicity, let's call them 'Legion' ... if you catch the reference. They have ALWAYS been a total nightmare from .... well if you caught 'Legion', then you know. Would you like to see something scary? Sign into you 'Legion' account on the web then go here: https://outlook.live.com/mail/options/mail/brandsSubscriptions Some are ones YOU signed up for. Others are ones THEY signed you up for. Not a lot of people know about this little list in OUR email. Considering a switch to Gmail to end the nightmare.