I thought I'd stick this discovery here in the hopes that others would find it useful. I love Mozilla's Thunderbird email client. It does everything I want it to, including PGP/GPG via Enigmail, Calendering via Lightning, and Google contacts and Tasks via the Provider for Google Calendar extension.
But I just couldn't get it to get all my folders to sync on Mint GNU/Linux. Only the top level INBOX would download.
Turns out a "smart" engineer at Fastmail changed the auto-configure IMAP SSL port from 993 to 992 to get Thunderbird to work better with some non-compliant email programs, including Apple's Mail. I had tried every possible solution including subscribing to specific folders and renaming the root folder until I found this post:
It's a clever hack that makes Fastmail work better for Apple, Windows, and Blackberry users but it confuses the heck out of compliant client users who allow Fastmail to auto-configure settings.
Changing SSL port 992 to 993 fixes the problem.
It's okay to use the autoconfig - it works fine otherwise - but if you're not getting all your mail try switching ports. 993 is standard, 992 is a hack for some non-compliant clients.