if you "x" button exit the window, it is going to be closed when you log in next. if you issue the show command, we update that you want to show it next time.
if you changed any files to "read only" so files can't be updated/changed, then they would not change, for some reason people do this then are curious why settings don't save.
if you are having your MQ files getting scanned or locked by AV/defender, you could also have an issue where it can't read/write them appropriately.
otherwise when you /mag show - and that window is now open, that window is saved in that state, that you want that window shown upon logging in, or reloading your ui - zoning etc - we do.
to load or not is saved in the "MQ2Mage.ini" inside your config folder (NOT inside the cwtn folder).
Here mage 1 and 2 would have their window shown, mage 3 would not
INI:
[General]
FontSize=font 4
[Mage1]
Show=1
[Mage2]
Show=1
[Mage3]
Show=0
if your mq output is going to your regular window it is because you have mq2chat loaded. unload mq2chat if you don't want mq going to your eq chat windows
/plugin mq2chat unload >>> read here <<<