The problem is in campaign mode.
To recreate in the debug console you need you need to turn "achbeesgone" to true and add at least 1 to Totalthingies,
press enter (or start on a 2nd pad) to add 2 player the go to the right and talk to the creepyguy with F (or square on ps pad) and walk right until it starts campaign mode.
Ive narrowed it down to ive probably done somthing with the layer that i didnt realise and it has saved the problem to the save state file and that why its been so hard to figure out.