I am having a similar issue recently. I have many Outlook windows open - reminder, reading an email, creating an email or calendar invite - and I notice I don't have the "main" window and I am unable to natvigate to next task without right clicking the Outlook icon in task bar and selecting Outlook - then the main window is back. I can't seem to determine when/why this is happenning. It is very noticeable and impacts my ability to navigate.
It may be after a reminder comes up. Also I don't have the same menu with "hide when minimized" - but I will keep looking for it or check to see if the main window slid off screen.
Thank you.
Update: The Main Oulook Window has not slid off screen - When I hover by Outlook icon on task bar - three possible windows were dispalyed, if I used Alt-Tab to cycle through available windows for all apps - the same three Outlook Windows were available via that method as well.