That count would include the junk and trash folders. Are they not having unread mail in them?

The only folder with "unread" mail is Drafts, which has one item. No other folders or subfolders have unread counts.

I have repaired all of the standard Thunderbird folders, no change.

I have several dozen mail folders and subfolders, so I really don't want to have to run repair on every one of them, particularly since I don't really expect it to make a difference.

This is an error that did not exist until Thunderbird 91 changed my profile.

Try running a file > compact on all folders, a side effect of that is a new MSF file so your counts will all be reset in each folder.

A do not get you issue with it not being apparent in the last version. The message count was not shown in the previous version on the taskbar icon. OR are you using an addon or other non standard configuration?

The new mail icon used to go away when there was no unread mail, which means that I did not have 28 unread messages in the previous version.

I compacted every folder and restarted Thunderbird. Icon still shows 28 unread messages.

Unread count still wrong on 91.0.1. I am just going to disable the icon until I am aware of a fix.

I have the same problem, on two Windows 10 PC's . Have deleted every msf file to no avail. Both PC's indicate 26 unread messages when TB says there are none.  ??? See attached screenshot.

@Joe-fitz That is an image of your inbox, really that means nothing as it should be counting all messages in the folder pane that show unread.

I have not had time to look into the issue in any depth. It really does not affect me as my icon shows 99+ permanent and probably will for ever. I have some 22 thousand unread messages in my inbox

I would guess the figure is at least in part comprised of unread message in the account reported by the server for IMAP accounts and that may include mail in unsubscribed folders and others that are not checked unless you select them, like junk/spam and trash/deleted.

The new option in 91.0.2 to remove the count from the tray icon basically accomplishes nothing, because the icon still shows that there is unread mail, even when there isn't.

Right-click the affected folder in the folder pane - Mark Folder Read

If you had read my original post, you would know that there IS NO AFFECTED FOLDER.

Prior to 91, I had no unread mail. I now consistently have 28, according to the tray icon, but in reality, there isn't any. There is no unread mail in my folders or on either server.

91 is seeing something that 78 did not see, and the evidence suggests that 91 is wrong.

There is a fix in TB 91.0.3: Unread message count badge on Windows tray icon did not update after moving messages to the Junk folder

Unfortunately, 91.0.3 did not fix my problem. I still show 28 unread messages.

Where else can I look for these "unread" messages? As previously described, they are not in any of my Thunderbird folders and not on either mail server (Gmail and Yahoo). I have done "mark unread" on everything without success. All Junk, Trash, and Spam folders are empty.