In a previous incarnation of Cubase - if you pressed Control + S, then closed the project too quickly, you would be asked if you wanted to save the project (again) So I got used to counting to 3 and then closing it. It seems to me like this bug is back again. Doesn’t seem to be an issue if you choose Save from the menu. But if I use Control + S, then use the mouse to close the project, I get a Save prompt.
Are you sure this happens only if you Close project very quickly after Save?
Some plug-ins are constantly sending own values. If you are using any of these plug-ins, Cubase always asks to Save the project while you Close it.