We always have to use an Autorun Macro to enable Reference Level Overrides for every session because we alsways want to save Reference Level states in our container files. Addition of a variable that allows this to always be turned on would make it much easier for users to manage reference levels without having to use custom processes.
Our level overrides are always on... I think if you turn them on in your seed file(s) the problem will be solved. That's what we did. It's possible your process is unique though and this wont work.