Logging in loads charpane.php, refreshing loads api.php. Not that things can't be changed, but that's the current difference.
LoginRequest.processLoginRequest() calls LoginManager.login() which calls LoginManager.doLogin() which calls LoginManager.initialize() which calls KoLmafia.refreshSession() which calls KoLmafia.refreshSessionData() which calls ApiRequest( "status" )Logging in loads charpane.php, refreshing loads api.php.
Not based on looking at any code, but perhaps daily variables are reset to default values after the ApiRequest call? That would only happen the first time a character is logged in for the day.