Before anything else, make sure to have a full backup of the Thunderbird profile. https://support.mozilla.org/kb/profiles-where-thunderbird-stores-user-data#w_backing-up-a-profile

I am unable to subscribe to All Mail in Gmail.

What do you need "All Mail" for in Thunderbird? If you're not subscribed to "All Mail" now, then I'd leave it alone.

The mixing of messages seems to indicate corruption of the database.

Indeed. Anti-virus software is the most likely the culprit for causing mail file corruption. What is your anti-virus software?

These are some generic suggestions to avoid problems with anti-virus software.

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

Don't let your anti-virus software scan incoming and outgoing messages.

Don't let your anti-virus software scan attachments.

Don't let your anti-virus software intercept your secure connection to the server.

Remove any add-ons your anti-virus software may have installed in Thunderbird.

Keep it working. http://kb.mozillazine.org/Keep_it_working_-_Thunderbird

And last but not least, backup your Thunderbird profile on a regular basis. https://support.mozilla.org/kb/profiles-where-thunderbird-stores-user-data#w_backing-up-a-profile

one difference is that somehow this machine is on the beta channel and the other uses the release channel.

It's because you installed the beta version at some point. Whether this was intentionally or not is a different story. In any case, the beta version isn't the cause of the problems you have. So leave it as is for the time being.

I don't want to lose my long email history ...

Creating regular backups of the Thunderbird profile will prevent that.

I explained why I need to see All Mail in my original message. Please do not challenge a legitimate need of mine which is supposed to work properly but does not.

I am using Malwarebytes premium and I do not see any options in there to specifically disable email protections. I have gone through all user-accessible menus and options. There is no thunderbird add-on that I can see.

Just today I re-opened an email I received a few days ago and it is now corrupted. The same email on the other system using thunderbird is fine.

One more symptom: thunderbird frequently just stops responding for 5-10 seconds. If I am typing and it freezes, the characters appear after the delay. No other programs on this machine do this and I do a lot of work on this machine (many hex editors, Excel, pdf readers and editors, word, visio, you name it). Only thunderbird does this. When I run task manager I see thunderbird starts taking around 10% processor utilization up from a couple percent when this is happening. Every other program on this machine works just fine.

Yes, I do backup my profile (and everything else) but what good does that do if thunderbird can't use it? I need a fix for the problem.

Is it possible to export the entire message database into some other format, like for another email program, then create a new profile in thunderbird and import it? That might be a way to rebuild the database.

I send files and lists to myself from the other machine but Gmail won't show them in the inbox. Instead, they only show in All Mail.

They show up in the Sent folder. This is how Gmail works, and has got nothing to do with Thunderbird.

I explained why I need to see All Mail in my original message. Please do not challenge a legitimate need of mine which is supposed to work properly but does not.

It is entirely up to you to follow suggestions or not. If not, it may not help you resolving your problems though.

I am using Malwarebytes premium and I do not see any options in there to specifically disable email protections.

You'd need to contact Malwarebytes to get help with their product.

As a troubleshooting step, you can try to start Windows 10 in safe mode with networking enabled. Windows safe mode disables anti-virus software.

Try again to repair mail files while in Windows safe mode. Is there any difference?

Even if your antivirus software worked great for months or years, across many previous versions of Thunderbird, this is NO guarantee it is working correctly now. Antivirus and Thunderbird have a complex relationship, and that relationship can be broken by updates or version changes of either software. Yes even if Thunderbird is the only software affected, even if your AV version did not change. AV vendors don't always play nice, and don't always adapt their software to new versions of other software on your computer, whether you know it or not they do make accommodations under the hood for how they interact with other software. In short, if TB performance is good when AV software has been disabled, doesn't make this fundamentally a bug in Thunderbird, although there are certainly areas of Thunderbird performance that can be improved.

The Sent folder is too corrupted to open messages so I cannot determine if you are correct. TB just hangs and I have to force close.

Yes, I know how Gmail works (I mentioned this in my message) but I also know that thunderbird should be able to have All Mail as a folder. I know this because this works perfectly on my other machine.

It takes 3-4 days to have thunderbird do a complete repair and I am reluctant to run my system in unprotected mode that long just as a test. Malwarebytes has confirmed that my configuration is not testing emails at this time so that is unlikely the issue anyway. In any case, the same Malwarebytes is running on the other system without any problems.

How about my idea of backing up all my emails to a neutral text format and then creating a completely new profile and importing then from that neutral format? Why won't that work and get me an essentially clean database?

I have now been able to determine that you are incorrect about the messages I send to myself from another computer showing up in the Sent folder.

It appears to me that thunderbird becomes unstable with large amounts of history. It may work well with small email accounts but for larger amounts of email it may not work well.

Update: All of my problems are indeed due to actual Thunderbird bugs in the latest beta versions. I am running on the release version 91 now and all seems well.