MacroQuest overlay position/information is stored in the MacroQuest_Overlay.ini in your config folder. This is something that MacroQuest does automatically for all of the overlay placement/positions (this is all things imgui - like the new cwtn ui window, or any of the other overlays that you find now like boxhud, buttonmaster, portalsetter window, or guildclicky, etc.)
what appears to be happening for some folks, is an issue creating entries for all of your toons when they all enter the game at the same time. when that happens - for some folks - there ends up being a "file locking" issue, where the file is busy being written to by something else, so it can't be written to by the other toons coming in.
Using ISBoxer to launch, which launches toons 1 by 1 appears to help avoid this because each toon entering the game is staggered.
if you have an old hard drive or do file scanning (like AV), or file syncing, this can exacerbate this issue - but unfortunately not something that we can do about that either. :'(
Another thing that has been happening to folks who use ISBoxer with window tiling - is when you swap which tile has focused, it does something where the other tile gets resized which causes imgui to mess with the position of the window you just had as if you moved it - unfortunately this is ISBoxer doing that, and not something that MQ can do anything about.
re: mode - yes if you zone it changes from a pulling mode to the respective non-pulling mode, it tells you in the output window. you should 1000% not instantly start pulling the moment you log in - if you wanted to do that you could use a .cfg