To diagnose problems with Thunderbird, try the following:

• Restart Thunderbird with add-ons disabled (Thunderbird Safe Mode). On the Help menu, click on "Restart with Add-ons Disabled". If Thunderbird works like normal, there is an Add-on or Theme interfering with normal operations. You will need to re-enable add-ons one at a time until you locate the offender.

Thanks, Matt, but it didn't solve the problem. I had only one add-on enabled (Mail Merge). Now it has been also disabled, but the problem persists.

How is the Ignore Thread flag set to the message? Is it something you can see in View > Message Source like in the X-Mozilla-something field?

https://support.mozilla.org/en-US/kb/ignore-threads

Usual method: Right click on that email in list and select 'Ignore subthread' what happens? Or select the email and use 'shift' + 'K' key Or select email 'Menu icon' > 'Message' > click on 'Ignore subthread' which should be selected if you have selected the email marked as such.

Hi Toad-Hall, > Right click on that email in list and select 'Ignore subthread' what happens? Nothing seems to happen to the message itself. 'Replies to the subthread "Photo meetup / drone" will not be shown. [Learn More...] [ Undo ignore Subthread]' is shown every other time. The "Ignore Subthread" menu item in the Message menu *from the menu bar* gets the check mark every other time. The same menu in the right-click popup never shows the check mark. The icon on the leftmost column on the message never disappears.

This is true with certain messages in my Inbox like the one shown in the screenshot in my first post. The flag toggles correctly for other messages.

How is the Ignore Thread flag set to the message? Is it something you can see in View > Message Source like in the X-Mozilla-something field?

re : This is true with certain messages in my Inbox

To rule out a corrupted 'Inbox' folder issue:

• Create a new folder called eg: 'Old Inbox'.
• Move all good emails from 'Inbox' to 'Old Inbox' folder.

I'm asking you to move emails before compacting as compacting on a corrupted folder could result in dataloss.

• right click on 'Inbox' and select 'Compact'.

• Select 'Old Inbox' folder.
• right click on email and click on 'Ignore Subthread' option.

Please report back on results.

I finally figured it out.

I selected View > Sort by > Threaded. Now the ignored subthread messages lined up in the thread tree (i.e., indented subjects). *Only when I had the very first message in the ignored subthread selected*, the Ignore Subthread toggle menu worked. Problem solved.

I always use the View > Sort by > Unthreaded mode. So, it was hard for me to see the first message in the ignored subthread and to know the toggle menu would only work with the first message.

So, it's technically a user error but I believe it's possible for many users to hit K or Shift-K by accident and have some messages disappear on them when "Ignored Thread" menu is unselected.

Is it possible to optionally disable these keyboard shortcuts? Thanks.

Found a solution for disabling keyboard shortcuts myself: http://unix.stackexchange.com/questions/141523/disable-keyboard-shortcuts-in-thunderbird

Just me, but that information is available in the Thunderbird knowledge base. See https://support.mozilla.org/en-US/kb/keyboard-shortcuts#w_customizing-keyboard-shortcuts