Try to start Windows in safe mode with networking enabled. - Win10 https://support.microsoft.com/en-us/help/12376/windows-10-start-your-pc-in-safe-mode - Win8 https://support.microsoft.com/en-us/help/17076/windows-8-startup-settings-safe-mode - Win7 https://support.microsoft.com/en-us/help/17419/windows-7-advanced-startup-options-safe-mode#start-computer-safe-mode=windows-7

Still in Windows safe mode, start Thunderbird in safe mode. - https://support.mozilla.org/kb/safe-mode

Does the problem go away?

No, the problem didn't go away and in fact, it got worse. The original problem is primarily when I reply. In safe mode I cannot send at all. Instead, I get a message saying there's a problem with the server. I also cannot save a messages as a draft.

The key is: start Windows in safe mode with networking enabled.

Sorry, I didn't see that. However, after I restarted in normal mode there have been two changes: First and most importantly, I have been able to reply successfully. Second, a "reply to sender only" box isn't present. That is not a problem, just a change.

In case the 'Not responding' issue pops up again:

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. http://kb.mozillazine.org/Profile_folder_-_Thunderbird

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