I have no idea where to look anymore. Drewn shapes like rectangles, squares do not appear. I checked Opacity and masks. There is no other Object in the file.

nevermind. preferences.xml had to be deleted. this is a very annoying bug that will put off less advanced users from using inkscape. errors without error messages or visual indicators are a big nono, for commercial software as well as for open source software. at least from someone who wants to use those tools in a production environment.