If one opens Project/Text Preferences in Full Screen mode, the Scrivener main window and the full screen mode coexist. To replicate the problem, simply follow these two steps:
- enter in Full Screen mode
- Go to the Project menu, then Text Preferences…
I think this is an odd behavior, I would not expect full screen to remain as a background, but it has no functional consequences as far as I can see.
In any case, S2 is great.