Not sure about the closing everything issue. I’ve not had that. But for graphical issues; it often helps to restart cinnamon by pressing alt-F2 (or sometimes Fn+alt+F2), typing “r”, then pressing enter.
Not sure if that would help for the kind of problems you’re having though.
Does Katawa Shoujo count? It’s not quite FOSS, but it’s a renpy game under CC BY-NC-ND.