Odd Window Minimizing Problem

Have you tried starting in Safe Mode and see if the problem still occurs?

Restart holding the "shift" key.

(Expect it to take longer to start this way because it runs a directory check first.)

If this works look in System Preferences > Users & Groups > Login items and delete any third party login items (-), you can always add them back with the (+). Also look in /Library/Startup Items. Nothing is put in that folder by default, so anything in there is yours.

You haven't somehow gotten them all in separate spaces, have you? How does Mission Control show them?

Pointing me back to System Preferences | Mission Control helped me fix this.

I had to turn "Group Windows by Application" back on, then my windows stayed open on the desktops.

I've gotten used to 4 finger swiping to switch desktop spaces.

thanks