I never use the autoECO function that pops up when you open a max file. I prefer to control it manually thru the AutoECO function. There are several options in the AutoECO menu and you have to use some care in choosing. The plain AutoECO selection (top of menu) is only for component and net additions and deletions and does not consider attribute changes -including footprint changes.
I typically use the AutoECO Override Attributes selection as this catches all changes including footprints, values, ect. If the scm is properly up to date ie. recently back-annotated with layout swp file, ECO changes made to scm and then the AutoECO O/R/A run, there shouldn't be any problems.
Not sure if that helps...
Ron O