By the way, I've also tried creating a new profile and using that and I still have the problem.

I am using TB 45.4.0 on Windows 10.

Thanks, Bill

You may find that those folders don't actually update until you look at them. Therefore the count includes only what is currently in Thunderbird's local copy of the folder and not what is still on the server waiting to be downloaded.

This wouldn't happen with POP because all the folders are handled locally and there can be no pending message to account for.

If I have Thunderbird set to check for mail every 3 minutes, shouldn't this be downloading these emails so that there should be no need to look at the folder to update it?

Thanks, Bill

My experience after setting-up an existing email account with many subfolders was that these didn't populate until they were explicitly opened.

Your 3 minute interval is rather ambitious and aggressive. Some mail provers would give you error messages and tell you to increase the interval to 15 minutes. But most IMAP is now implemented as a "push" service and largely ignores those refresh settings anyway, and in this case you might be at the mercy of the server configuration as to which folders it pushes.

There may be settings in the folder properties to "include this folder when fetching new mail", though ISTR this setting is specific to POP-connected accounts.

I guess I'm confused as to why Thunderbird doesn't flag them as new messages when eM Client does on my PC and TypeApp does on my phone and tablet. The messages are sometimes delivered in the middle of the night and when I look first thing in the morning, the counts are not updated in TB but they are everywhere else. My guess is that they are there in Thunderbird, but for some reason TB is not updating the counts. In fact, it isn't even bolding the folder as it usually does when a folder contains new messages.