Our current configuration uses "cam5" physics and applies the surface fluxes after coupling in tphysac. In E3SMv1 using CLUBB, sensible and latent heat fluxes are applied in CLUBB (in tphysbc). Currently, when configuring SP to use "clubb" physics, SHF and LHF get "forgotten" after clubb runs, so this forcing doesn't get felt by the CRMs.
Temporary solution: Don't use CLUBB with SP1.
ToDo (sooner): Add logic to call endrun if model is configured in this way.
ToDo (later): Fix?