I have had to setup my chat window settings so many times I have lost count. Not sure when this started but all I can tell you is that the checked boxes are resetting and it is in chat window 3 and 4. Chat windows 1, 2 and 5 for some reason do not change ever, they are still the way I set them up from way way back. I have searched for fixes but I can't find anything related to what is happening here. I have noticed one instance of it happening is when I am changing UI presets but this is not the case everytime they reset.

For me, this happens on reload / when I change UI presets, but only if you did not include the new chat window setup in the UI preset. So what you can try is set up your chat windows as you want, and then saving that to your UI preset (all of them, including the general settings), and seeing if that fixes it.