Aside from playback needing to be stopped, Auto save is triggered only when there are unsaved changes, so if you are exploring your project and not making changes when the 3 minutes are up it does nothing.
The behavior described is what happens if you do not make any changes that would be saved in the project.
It could also be that one of your settings files is corrupt, in which case you should start Cubase in safe mode and see if it still occurs.