This 'sounds like' the prefs.js file is not being allowed to be saved when thunderbird closes. This might be if the file is read-only or if some other software is interferring. This is not a diagnosis, but what you describe fits that particular issue.

Just wondering if that explains this also happening at first? I had a bunch of accounts in there and they persisted across close, but then I updated Thunderbird and all but the top one disappeared.

I'm wondering this because if prefs.js isn't saved when Thunderbird closes then it sounds to me like that could explain not persisting new additions, but not the removal of previously persistent accounts.

Exactly. Thunderbird makes all changes in memory, even simple tweaks, and saves them in prefs.js when closed. You might check your profile to see if there are multiple copies of the prefs.js file. if there are (e.g., prefs-1, prefs-2, etc) you could delete all except the one with highest number and then rename that one to prefs.js. This happened to me and I found my prefs.js was read-only, causing the problem. But others have had the problem when anti-virus interferred - or other causes.

Check Error Console (ctrl+shift+J) after startup for errors, and post them here.