User Agent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/72.0.3626.109 Safari/537.36

Steps to reproduce:

A1. PRECONDITION: Unknown adaptive junk mail setting (try both in config file before starting Thunderbird-- you may therefore have to execute this checklist twice); probably disabled.
A2. In the accounts list, RIGHT-CLICK an account name (e.g., yadda@whatever.com), and LEFT-CLICK "Settings" from the pop-up menu.
A3. In the "Account Settings" dialog, LEFT-CLICK "Junk Settings" for the same account.
A4. OBSERVE PRECONDITION: "Enable adapative junk mail controls for this account" is CHECKED.
A5. OBSERVE: All options in the "Do not automatically mark mail as junk if the sender is in" subsection are DISABLED (GRAYED OUT) even though the checkbox next to "Enable adaptive junk mail controls for this account" is CHECKED.
A6. LEFT-CLICK the checkbox next to "Enable adaptive junk mail controls for this account".

Evaluate results AR and expected results AX below.

After following sequence A and observing results AR and reviewing expected results AX, follow this sequence:

B1. LEFT-CLICK the checkbox next to "Enable adaptive junk mail controls for this account". (NOTE: This will be the second click on this control since this dialog box has been opened if you have followed sequence A and observe result set AR before performing this action.)
B2. OBSERVE: The "Enable adapative junk mail controls for this account" checkbox has become CLEARED.
B3. OBSERVE: All options in the "Do not automatically mark mail as junk if the sender is in" subsection are DISABLED (GRAYED OUT).
B4. EITHER click on any other account OR click OK to close the dialog.
B5. EITHER LEFT-CLICK "Junk Settings" for the account you initially used OR re-open the dialog and LEFT-CLICK "Junk Settings" if you have only one account.

Evaluate results BR and expected results BX below.

Actual results:

AR1. OBSERVE: The checkbox next to "Enable adaptive junk mail controls for this account" REMAINS CHECKED.
AR2. OBSERVE: All options in the "Do not automatically mark mail as junk if the sender is in" subsection have become ENABLED (UNGRAYED) even though the "Enable adaptive junk mail controls for this account" checkbox has not visibly changed state.

BR1. OBSERVE: The "Enable adapative junk mail controls for this account" checkbox has insubordinately become visibly CHECKED.
BR2. OBSERVE: All options in the "Do not automatically mark mail as junk if the sender is in" subsection remain DISABLED (GRAYED OUT) even though the "Enable adaptive junk mail controls for this account" checkbox has become visibly CHECKED.

Expected results:

AX1. The checkbox next to "Enable adaptive junk mail controls for this account" should, on a single left-click, TOGGLE STATE to become UNCHECKED.
AX2. At step A5, all options in the "Do not automatically mark mail as junk if the sender is in" subsection should have been ENABLED (UNGRAYED) because the checkbox next to "Enable adaptive junk mail controls for this account" checkbox was visibly CHECKED.

BX1. The "Enable adapative junk mail controls for this account" checkbox should obediently REMAIN UNCHECKED.
BX2. At all times, the options in the "Do not automatically mark mail as junk if the sender is in" subsection should be DISABLED (GRAYED OUT) IF AND ONLY IF the "Enable adaptive junk mail controls for this account" checkbox is visibly UNCHECKED.

0. QA: Please follow the the sequence above STRICTLY (set your PEDANTIC switch to MAXIMUM) as there are a bunch of recent, dismissed bugs that I strongly suspect are this bug, but have been casually dismissed because the sequence did not clearly call out EXACTLY what was going on. This sequence, if followed EXACTLY, is highly reproducible. Please follow it PRECISELY, so that we can get this caught and shot.

1. DEV: This behaves suspiciously like a checkbox that is intended to be bi-state, but has been instantiated as tri-state.

2. DEV: POSSIBLY reference bug 1281733, which is closed, but MAY be informative.

Platform is Fedora 29 64-bit. GUI is GNOME 3.

Sorry it took so long to get to this bug. We're now at TB 68.1.2. Does the issue still happen there?

Matt, do you still see this issue?

Matt seems to be gone

I ended up here while planning to file a new bug for v78 (78.0.1). I can confirm that I have reproduced this behaviour when changing the adaptive junk mail controls setting for three freshly setup IMAP (Gmail) accounts in a freshly created profile. The checkbox reverts back to checked, despite countless attempts to uncheck it. My desire is to disable adaptive junk mail controls for these accounts and rely on SpamAssassin and Gmail's spam filtering. This bug does not affect my v68 installation. A similar bug that affects advanced server settings has resurfaced in v78, as reported here bug 160644 and encountered in the forum question here https://support.mozilla.org/en-US/questions/1295989

I'm going to suggest this has been fixed by bug 1607613 in 78.1.0.
Feel free to disagree.