Wel that's annoying. No sense using the flip case if flipping it activates the screen mode.
Are you completely flipping the cover to the rear of the phone? If so, yes, that can trigger the "windowed" mode. I don't recall if the official BB case did that both some other brands did have that affect on the screen.
GF has official BlackBerry case with window and flipped to back does not trigger window mode & used in front reduces and expands when opened... may be too strong magnet in other maker's items?