Check to see if your antivirus or vpn is interferring with thunderbird. What you are describing is a situation where thunderbird is being prevented from shutting down successfully. That is when the prefs.js file in the profile is updated with all updates from current execution. It might also be a situation where the prefs.js is read-only. If you browse the profile and see multiple instances of the prefs.js, that is also an indication of interference during shutdown. Please post results.

Thank you David. There are 40 prefs files in my profile folder, all dated more than a year ago but the problem only appeared this week after I added the new email account. I have had McAfee installed and operating for several years with no problem but I don't know how to check if it is interfering. I don't have a vpn turned on. Any suggestions?

First, there is a problem and something is messing things around - but that's above my pay grade. To fix what you have, my guess is that your latest updated prefs-x.js has the content you want. So, delete all prefs files except the highest numbered one, and rename that one to prefs.js. Based on feedback from others with the same problem, you may need to copy the highest-numbered prefs to a separate directory, rename it there to prefs.js, and then copy/paste into the profile. be sure thunderbird is NOT running during all of this. Do let me know results, as that helps when advising other users. Thank you

I followed your instructions, renaming the newest prefs file in another folder and and replacing it back in the profile. Then I opened Thunderbird and added the new account again, it loaded as expected and all went well. I closed Thunderbird and after waiting briefly opened it again...but the new account did not appear. My other two were there and working as usual.

To avoid problems create an exception in your anti-virus software for the Thunderbird profile folder, so that the anti-virus real-time scanner will not scan it. https://support.mozilla.org/en-US/kb/profiles-where-thunderbird-stores-user-data#w_how-to-find-your-profile

Does the problem go away?

My McAfee will not allow me to exclude the folder, it only seems possible for me to exclude an individual file on a temporary basis. Anyway I disabled real time scanning altogether to see if that helped, and no, it doesn't. With real time scanning turned off, the newly added email account does not reappear if I close Thunderbird and then reopen it.

I have had McAfee installed and operating for several years with no problem but I don't know how to check if it is interfering.

I would suggest removing it, it has been causing significant issues with email receipt since at least 2012 when they introduced their new heuristics engine. I gave up updating the linked page a number of years ago, but it illustrates the problem with McAfee specifically and antivirus generally. https://wiki.mozilla.org/Thunderbird:Testing:Antivirus_Related_Performance_Issues#McAfee

If you are to stay with it, I suggest you created an exception in your antivirus for the Thunderbird profiler folders as it can't stop messing with things that are of no concern to it. McAfee offer instructions. It may take hours to do a whole folder and the exclusions apparently only remain until after the file changes. https://www.mcafee.com/support/s/article/000001661?language=en_US although this brief page indicates you can exclude folders. But as I eschew use of paid commercial antivirus I have no recent first hand experience. After more than 25 years paying various providers I bit the bullet and decided to give Windows defender a go when I purchased my latest PC. It rates well on the various "best of" tests and I was sick of messing with things that were not broken until the antivirus got involved. I am still happy some years latter.

This article offers instructions on how to disable real time scanning, the probable cause of this issue and a myriad of others where Thunderbird settings and setting changes are not saved. https://www.mcafee.com/support/s/article/000002088?language=en_US

Note that if you uninstall McAfee, Defender will automatically replace it on windows 10 and 11. Allthe alarmist statements on the McAfee web site are just that alarmist marketing information designed to scare folk into handing over their money and staying "safe".

I recommend uninstalling, but there is always restarting the operating system in safe mode with networking to exclude third party software of most kinds that loads with the operating system. Unfortunately these days most folks use laptops that are connected via WiFi and operating systems do not have WiFi in safe mode with networking. A wired internet connection is a necessity for diagnostics using that mode and many simply do not have the capability.

If you do have the capability Microsoft offer instruction on how to enter that mode here https://support.microsoft.com/en-au/windows/windows-startup-settings-1af6ec8c-4d4a-4b23-adb7-e76eef0b847f