You heard the title, basically my timer automatically starts ONLY on Anomalous Materials and not on other levels when I want to run individual levels, it also doesn't autostart on the Hazard Course. Help would be appreciated :)

I'm aware I may be a bit late to help, but if you go into settings there's an "Also autostart when..." option. You can just set it to autostart when starting a new game on the first map of the chapter you want to run.