Every time I start it, the settings change and it goes into windowed mode.

I have a question.  In fc26 companion app.  When i press my back button at bottom of screen it minimises the app.   It used to go back to previous page on the companion app and then back again would go back further in app.  Just shuts the app  

I have the exact same issue, and I have and AMD GPU

I play one two pcs one has amd the other nvidia both launch in windowed mode every time. Also if I have custom graphics settings such as all ultra and ray traced ambient occlusions. It defaults my graphics settings to ultra. Whatever render setting you have your custom set to, all other setting will be the same.

I recently changed to AMD. Did you end up finding a fix?